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- PDB-2csu: Crystal structure of PH0766 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2csu
TitleCrystal structure of PH0766 from Pyrococcus horikoshii OT3
Components457aa long hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyrococcus horikoshii / PH0766 / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


acetate-CoA ligase (ADP-forming) / acetate-CoA ligase (ADP-forming) activity
Similarity search - Function
Acetate-CoA ligase [ADP-forming], alpha domain / Ligase-CoA domain / Ligase-CoA domain / Succinyl-CoA synthetase-like, flavodoxin domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase domains / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding ...Acetate-CoA ligase [ADP-forming], alpha domain / Ligase-CoA domain / Ligase-CoA domain / Succinyl-CoA synthetase-like, flavodoxin domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase domains / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetate--CoA ligase (ADP-forming)
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH0766 from Pyrococcus horikoshii OT3
Authors: Sugahara, M. / Kunishima, N.
History
DepositionMay 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 457aa long hypothetical protein
B: 457aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)100,9862
Polymers100,9862
Non-polymers00
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-28 kcal/mol
Surface area33190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.459, 70.589, 88.514
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer (chain A and B) in the asymmetric unit.

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Components

#1: Protein 457aa long hypothetical protein


Mass: 50493.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58493
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.7 / Details: PEG4000, pH 4.7, microbatch, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.54178
SYNCHROTRONSPring-8 BL26B120.97925, 0.97954, 0.97700, 0.98300
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEFeb 4, 2005
RIGAKU JUPITER2CCDApr 20, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
20.979251
30.979541
40.9771
50.9831
ReflectionResolution: 2.2→20 Å / Num. all: 45198 / Num. obs: 45198 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 37.383 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.101 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.91 / Num. unique all: 4486 / Rsym value: 0.529 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.85 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2244 -RANDOM
Rwork0.246 ---
obs0.246 45008 99.9 %-
all-45008 --
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.44 Å20 Å2-0.26 Å2
2--1.16 Å20 Å2
3---9.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6671 0 0 460 7131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.018
X-RAY DIFFRACTIONc_bond_d1.4
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.34 210 -
Rwork0.323 --
obs-4250 99 %

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