3D4R | pdb_00003d4r

CRYSTAL STRUCTURE OF a DUF2118 family protein (MMP0046) FROM METHANOCOCCUS MARIPALUDIS AT 2.20 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3D4R/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Methanococcus maripaludis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-14 Released: 2008-07-08
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.193 (Depositor), 0.195 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Domain of Unknown Function from the Pfam-B_34464 Family (NP_987166.1) from Methanococcus maripaludis JJ (DSM 2067) at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 119.61 kDa
Atom Count: 8,079
Modeled Residue Count: 940
Deposited Residue Count: 1,014
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Domain of Unknown Function from the Pfam-B_34464 Family	A, B, C, D, E A, B, C, D, E, F	169	Methanococcus maripaludis	Mutation(s): 0 Gene Names: NP_987166.1, MMP0046
UniProt
Find proteins for Q6M171 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL)) Explore Q6M171 Go to UniProtKB: Q6M171
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6M171
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain P [auth F] SDF format, chain O [auth F] SDF format, chain N [auth E] SDF format, chain M [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] MOL2 format, chain N [auth E] MOL2 format, chain M [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F] mmCIF format, chain N [auth E] mmCIF format, chain M [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth C] J [auth C] K [auth D] G [auth A], H [auth A], I [auth C], J [auth C], K [auth D], M [auth E], N [auth E], O [auth F], P [auth F], Q [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.193 (Depositor), 0.195 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.877	α = 90
b = 109.858	β = 90
c = 135.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-08

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-07-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary

3D4R | pdb_00003d4r

CRYSTAL STRUCTURE OF a DUF2118 family protein (MMP0046) FROM METHANOCOCCUS MARIPALUDIS AT 2.20 A RESOLUTION

Literature

Crystal structure of Domain of Unknown Function from the Pfam-B_34464 Family (NP_987166.1) from Methanococcus maripaludis JJ (DSM 2067) at 2.20 A resolution

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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