3CTD | pdb_00003ctd

Crystal structure of a putative AAA family ATPase from Prochlorococcus marinus subsp. pastoris

PDB DOI: https://doi.org/10.2210/pdb3CTD/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Prochlorococcus marinus subsp. pastoris str. CCMP1986
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2008-04-11 Released: 2008-04-29
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.275 (Depositor), 0.281 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a putative AAA family ATPase from Prochlorococcus marinus subsp. pastoris.

Bonanno, J.B., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 48.32 kDa
Atom Count: 2,435
Modeled Residue Count: 308
Deposited Residue Count: 426
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ATPase, AAA family	A, B	213	Prochlorococcus marinus subsp. pastoris str. CCMP1986	Mutation(s): 1 Gene Names: yrvN, PMM0077
UniProt
Find proteins for Q7V3J8 (Prochlorococcus marinus subsp. pastoris (strain CCMP1986 / NIES-2087 / MED4)) Explore Q7V3J8 Go to UniProtKB: Q7V3J8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7V3J8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.275 (Depositor), 0.281 (DCC)
R-Value Work: 0.211 (Depositor), 0.211 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.184	α = 90
b = 108.184	β = 90
c = 68.685	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-04-29

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-04-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Structure summary
Version 1.5: 2021-10-20
Changes: Database references
Version 1.6: 2024-02-21
Changes: Data collection

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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.