3NEI | pdb_00003nei

Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus (no SAH bound)

PDB DOI: https://doi.org/10.2210/pdb3NEI/pdb

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

Deposited: 2010-06-08 Released: 2011-06-15
Deposition Author(s): Seyedarabi, A., Pickersgill, R.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.242 (Depositor), 0.240 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus (no SAH bound)

Seyedarabi, A., Pickersgill, R.W.

To be published.

Macromolecule Content

Total Structure Weight: 60.09 kDa
Atom Count: 3,459
Modelled Residue Count: 449
Deposited Residue Count: 562
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-4 C(11)-methyltransferase	A, B	281	Rhodobacter capsulatus SB 1003	Mutation(s): 0 Gene Names: cobM EC: 2.1.1.133
UniProt
Find proteins for O68100 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)) Explore O68100 Go to UniProtKB: O68100
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O68100
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.242 (Depositor), 0.240 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.046	α = 90
b = 54.499	β = 90
c = 175.85	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-06-15

Deposition Author(s):

Seyedarabi, A.

Pickersgill, R.W.

Revision History (Full details and data files)

Version 1.0: 2011-06-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

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Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus (no SAH bound)

Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus (no SAH bound)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

3NEI | pdb_00003nei