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- PDB-1wr2: Crystal structure of PH1788 from Pyrococcus horikoshii Ot3 -

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Basic information

Entry
Database: PDB / ID: 1wr2
TitleCrystal structure of PH1788 from Pyrococcus horikoshii Ot3
Componentshypothetical protein PH1789
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyrococcus horikoshii / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acetate-CoA ligase (ADP-forming) / ligase activity / ATP binding / metal ion binding
Similarity search - Function
: / ATP-grasp domain / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
acetate--CoA ligase (ADP-forming)
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH1788 from Pyrococcus horikoshii Ot3
Authors: Sugahara, M. / Kunishima, N.
History
DepositionOct 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PH1789


Theoretical massNumber of molelcules
Total (without water)26,8761
Polymers26,8761
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.346, 60.643, 96.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein PH1789


Mass: 26875.629 Da / Num. of mol.: 1
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: O59452
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.5 / Details: JAM, pH 6.5, microbatch, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B121.07172
SYNCHROTRONSPring-8 BL26B131.008
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATEJul 2, 2004
RIGAKU JUPITER2CCDOct 4, 2004
RIGAKU JUPITER3CCDOct 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.071721
31.0081
ReflectionResolution: 2→40 Å / Num. all: 18934 / Num. obs: 18934 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.04 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1852 / Rsym value: 0.647 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2→37.67 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 923 -random
Rwork0.228 ---
all0.228 18886 --
obs0.228 18886 99.7 %-
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å20 Å20 Å2
2---4.55 Å20 Å2
3---0.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→37.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 0 175 2036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.031
RfactorNum. reflection% reflection
Rfree0.291 86 -
Rwork0.3 --
obs-1719 97.5 %

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