1VL4 | pdb_00001vl4

CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF A DNA GYRASE (TM0727) FROM THERMOTOGA MARITIMA MSB8 AT 1.95 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VL4/pdb

• Classification: GENE REGULATION
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-09 Released: 2004-09-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold.

Rife, C., Schwarzenbacher, R., McMullan, D., Abdubek, P., Ambing, E., Axelrod, H., Biorac, T., Canaves, J.M., Chiu, H.J., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Hornsby, M., Jaroszewski, L., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Miller, M.D., Moy, K., Nigoghossian, E., Paulsen, J., Quijano, K., Reyes, R., Sims, E., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2005) Proteins 61: 444-448

• PubMed: 16104019 
• DOI: https://doi.org/10.1002/prot.20468
• Primary Citation of Related Structures:  
  1VL4

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Organizational Affiliation: 
• The Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 99.66 kDa 
• Atom Count: 7,177 
• Modeled Residue Count: 858 
• Deposited Residue Count: 894 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pmbA-related protein	A, B	447	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM0727
UniProt
Find proteins for Q9WZI6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZI6  Go to UniProtKB:  Q9WZI6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VL4

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.367	α = 90
b = 106.637	β = 90
c = 120.382	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
autoSHARP	phasing
SOLOMON	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references
• Version 1.5: 2024-05-22
  Changes: Data collection, Refinement description