3RPD | pdb_00003rpd

The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.

PDB DOI: https://doi.org/10.2210/pdb3RPD/pdb

Classification: TRANSFERASE
Organism(s): Shewanella sp. W3-18-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-04-26 Released: 2011-08-31
Deposition Author(s): Cuff, M.E., Li, H., Hatzos-Skintges, C., Tesar, C., Bearden, J., Clancy, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.189 (Depositor), 0.186 (DCC)
R-Value Work:
0.164 (Depositor), 0.163 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.

Cuff, M.E., Li, H., Hatzos-Skintges, C., Tesar, C., Bearden, J., Clancy, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 81.95 kDa
Atom Count: 6,494
Modeled Residue Count: 686
Deposited Residue Count: 714
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine synthase (B12-independent)	A, B	357	Shewanella sp. W3-18-1	Mutation(s): 0 Gene Names: Sputw3181_1250 EC: 2.1.1.14

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MSE Query on MSE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	SELENOMETHIONINE C₅ H₁₁ N O₂ Se RJFAYQIBOAGBLC-BYPYZUCNSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	E [auth A], H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
ZN Query on ZN 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] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.189 (Depositor), 0.186 (DCC)
R-Value Work: 0.164 (Depositor), 0.163 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.099	α = 90
b = 89.371	β = 92.45
c = 86.526	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary