4DCI | pdb_00004dci

Crystal structure of unknown funciton protein from Synechococcus sp. WH 8102

PDB DOI: https://doi.org/10.2210/pdb4DCI/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Parasynechococcus marenigrum WH 8102
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-17 Released: 2012-02-01
Deposition Author(s): Chang, C., Marshall, N., Bearden, J., Palenik, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.252 (Depositor), 0.233 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4DCI

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

Literature

Crystal structure of unknown function protein from Synechococcus sp. WH 8102

Chang, C., Marshall, N., Bearden, J., Palenik, B., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 135.72 kDa
Atom Count: 9,246
Modeled Residue Count: 1,168
Deposited Residue Count: 1,200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B, C, D, E A, B, C, D, E, F, G, H	150	Parasynechococcus marenigrum WH 8102	Mutation(s): 0 Gene Names: SYNW0670
UniProt
Find proteins for Q7U8F0 (Parasynechococcus marenigrum (strain WH8102)) Explore Q7U8F0 Go to UniProtKB: Q7U8F0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7U8F0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth F]	I [auth A], J [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [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, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.252 (Depositor), 0.233 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.181 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.272	α = 90
b = 164.522	β = 131.8
c = 105.421	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-01

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2012-02-01
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.