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- PDB-1wmm: Crystal structure of PH1033 from Pyrococcus horikoshii Ot3 -

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Basic information

Entry
Database: PDB / ID: 1wmm
TitleCrystal structure of PH1033 from Pyrococcus horikoshii Ot3
ComponentsHypothetical UPF0310 protein PH1033
KeywordsUNKNOWN FUNCTION / Pyrococcus horikoshii / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homologyUncharacterised protein family UPF0310 / EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta / UPF0310 protein PH1033
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Nucleant-mediated protein crystallization with the application of microporous synthetic zeolites.
Authors: Sugahara, M. / Asada, Y. / Morikawa, Y. / Kageyama, Y. / Kunishima, N.
History
DepositionJul 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 UPF0310 protein PH1033


Theoretical massNumber of molelcules
Total (without water)17,4651
Polymers17,4651
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.694, 95.694, 44.225
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer in the asymmetric unit.

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Components

#1: Protein Hypothetical UPF0310 protein PH1033


Mass: 17464.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58764
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.2 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.7 / Details: PEG4K, pH 5.7, microbatch, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B121.0079,1.0088,0.9900
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATEApr 9, 2004
RIGAKU JUPITER2CCDApr 3, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.00791
31.00881
40.991
ReflectionResolution: 2.2→40 Å / Num. all: 12147 / Num. obs: 12147 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 45.02 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.055 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1172 / Rsym value: 0.361 / % 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: MAD / Resolution: 2.2→32.48 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 582 -RANDOM
Rwork0.232 ---
obs0.232 12079 100 %-
all-12079 --
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1--12.22 Å2-2.58 Å20 Å2
2---12.22 Å20 Å2
3---24.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 0 45 1257
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.05
RfactorNum. reflection% reflection
Rfree0.328 43 -
Rwork0.338 --
obs-1142 100 %

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