1XET

Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA

PDB DOI: https://doi.org/10.2210/pdb1XET/pdb

Classification: TRANSFERASE
Organism(s): Pinus sylvestris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-09-12 Released: 2006-04-11
Deposition Author(s): Ng, S.H., Chirgadze, D., Spiteller, D., Li, T.L., Spencer, J.B., Blundell, T.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.223
R-Value Work: 0.195
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA

Ng, S.H., Chirgadze, D., Spiteller, D., Li, T.L., Spencer, J.B., Blundell, T.L.

To be published.

Macromolecule Content

Total Structure Weight: 181.29 kDa
Atom Count: 12,508
Modelled Residue Count: 1,540
Deposited Residue Count: 1,652
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropinosylvin synthase	A, B, C, D	413	Pinus sylvestris	Mutation(s): 0 EC: 2.3.1 (PDB Primary Data), 2.3.1.146 (UniProt)
UniProt
Find proteins for Q02323 (Pinus sylvestris) Explore Q02323 Go to UniProtKB: Q02323
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02323
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MCA Query on MCA Download Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	METHYLMALONYL-COENZYME A C₂₅ H₄₀ N₇ O₁₉ P₃ S MZFOKIKEPGUZEN-AGCMQPJKSA-N		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]
3IO Query on 3IO Download Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain G [auth D] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain G [auth D] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	E [auth B], F [auth C], G [auth D]	3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID C₁₁ H₉ N O₃ RSTKLPZEZYGQPY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.223
R-Value Work: 0.195
R-Value Observed: 0.195
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 54.465	α = 90
b = 111.19	β = 93.13
c = 132.015	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-04-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-04-11
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Advisory, Data collection, Refinement description
Version 1.4: 2024-02-14
Changes: Advisory, Data collection, Database references, Derived calculations

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1XET

Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA

Crystal structure of stilbene synthase from Pinus sylvestris, complexed with methylmalonyl CoA

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)