3U8V

Three dimensional structure of the Small Metal Binding Protein, SMBP

PDB DOI: https://doi.org/10.2210/pdb3U8V/pdb
Entry: 3U8V supersedes: 3DFB

Classification: METAL BINDING PROTEIN
Organism(s): Nitrosomonas europaea
Mutation(s): No

Deposited: 2011-10-17 Released: 2011-11-09
Deposition Author(s): Allen, J.P., Francisco, W.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.205
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Three dimensional structure of the Small Metal Binding Protein, SMBP

Allen, J.P., Francisco, W.A.

To be published.

Macromolecule Content

Total Structure Weight: 19.84 kDa
Atom Count: 1,356
Modelled Residue Count: 166
Deposited Residue Count: 186
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-binding protein smbP	A, B	93	Nitrosomonas europaea	Mutation(s): 0
UniProt
Find proteins for Q82S91 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82S91 Go to UniProtKB: Q82S91
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q82S91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.205
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.66	α = 90
b = 56.207	β = 90
c = 83.923	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-11-09

Deposition Author(s):

Francisco, W.A.

This entry supersedes: 3DFB

Revision History (Full details and data files)

Version 1.0: 2011-11-09
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.