3ND1

Crystal structure of Precorrin-6A synthase from Rhodobacter capsulatus

PDB DOI: https://doi.org/10.2210/pdb3ND1/pdb

Classification: TRANSFERASE
Organism(s): Rhodobacter capsulatus SB 1003
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-06-06 Released: 2011-06-08
Deposition Author(s): Seyedarabi, A., Pickersgill, R.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.220
R-Value Work: 0.194
R-Value Observed: 0.195

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Precorrin-6A synthase from Rhodobacter capsulatus

Seyedarabi, A., Pickersgill, R.W.

To be published.

Macromolecule Content

Total Structure Weight: 60.27 kDa
Atom Count: 4,530
Modelled Residue Count: 493
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Precorrin-6A synthase/CobF protein	A, B	275	Rhodobacter capsulatus SB 1003	Mutation(s): 0 Gene Names: CobF EC: 2.1.1
UniProt
Find proteins for D5AV00 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)) Explore D5AV00 Go to UniProtKB: D5AV00
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D5AV00
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B]	D [auth A], E [auth A], G [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.220
R-Value Work: 0.194
R-Value Observed: 0.195
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.661	α = 90
b = 89.283	β = 90
c = 107.163	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Seyedarabi, A.

Pickersgill, R.W.

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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3ND1

Crystal structure of Precorrin-6A synthase from Rhodobacter capsulatus

Crystal structure of Precorrin-6A synthase from Rhodobacter capsulatus

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)