3F7C

Crystal structure of a duf416 family protein (maqu_0942) from marinobacter aquaeolei vt8 at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb3F7C/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Marinobacter nauticus VT8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-07 Released: 2008-11-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.196
R-Value Work: 0.172
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of protein of unknown function (DUF416) (YP_958225.1) from MARINOBACTER AQUAEOLEI VT8 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 22.99 kDa
Atom Count: 1,714
Modelled Residue Count: 199
Deposited Residue Count: 200
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein of unknown function (DUF416)	A	200	Marinobacter nauticus VT8	Mutation(s): 0 Gene Names: Maqu_0942, YP_958225.1
UniProt
Find proteins for A1TZ69 (Marinobacter nauticus (strain ATCC 700491 / DSM 11845 / VT8)) Explore A1TZ69 Go to UniProtKB: A1TZ69
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1TZ69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.196
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: P 6₄
Diffraction Data: https://doi.org/10.18430/M33F7C

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.998	α = 90
b = 76.998	β = 90
c = 91.26	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: 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

Prepare Data

Validate Data

Deposit Data

Help and Resources

3F7C

Crystal structure of a duf416 family protein (maqu_0942) from marinobacter aquaeolei vt8 at 2.00 A resolution

Crystal structure of protein of unknown function (DUF416) (YP_958225.1) from MARINOBACTER AQUAEOLEI VT8 at 2.00 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)