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- PDB-2zbn: Crystal structure of PH1033 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2zbn
TitleCrystal structure of PH1033 from Pyrococcus horikoshii OT3
ComponentsUPF0310 protein PH1033
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyrococcus horikoshii OT3 / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / MOLECULAR REPLACEMENT / Resolution: 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
DepositionOct 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: UPF0310 protein PH1033


Theoretical massNumber of molelcules
Total (without water)17,4651
Polymers17,4651
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.035, 95.035, 44.536
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

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Components

#1: Protein 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) / Strain: OT3 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58764
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 295 K / pH: 5.7
Details: 22.5% PEG 4K, 15% Glycerol, 0.1M citrate buffer, pH 5.7, oil microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 15961 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.065 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1567 / Rsym value: 0.555 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1wmm

1wmm


Resolution: 2→39.17 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1334434.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 798 5 %RANDOM
Rwork0.244 ---
all0.244 15922 --
obs0.244 15922 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.7132 Å2 / ksol: 0.33759 e/Å3
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1--13.13 Å2-4.23 Å20 Å2
2---13.13 Å20 Å2
3---26.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 0 97 1309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.388 80 5.1 %
Rwork0.452 1483 -
obs-1483 99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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