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- PDB-2p62: Crystal structure of hypothetical protein PH0156 from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 2p62
TitleCrystal structure of hypothetical protein PH0156 from Pyrococcus horikoshii OT3
ComponentsHypothetical protein PH0156
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PH0156 / Pyrococcus horikoshii OT3 / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


PH0156-like / PH0156-like / PH0156-like domains / Protein of unknown function DUF3226 / Protein of unknown function (DUF3226) / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DUF4276 family protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsFu, Z.-Q. / Chen, L. / Zhu, J. / Swindell, J.T. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Chrzas, J. / Rose, J.P. ...Fu, Z.-Q. / Chen, L. / Zhu, J. / Swindell, J.T. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Chrzas, J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein PH0156 from Pyrococcus horikoshii OT3
Authors: Fu, Z.-Q. / Chen, L. / Zhu, J. / Swindell, J.T. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Chrzas, J. / Rose, J.P. / Wang, B.-C.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 PH0156
B: Hypothetical protein PH0156


Theoretical massNumber of molelcules
Total (without water)55,2652
Polymers55,2652
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-12 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.071, 122.071, 109.067
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Hypothetical protein PH0156


Mass: 27632.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0156 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: O57895
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.24 Å3/Da / Density % sol: 71.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.0 mg/ml) AND RESERVOIR SOLUTION CONTAINING 24% v/v MPD, 0.1M Sodium acetate (pH 4.8), 0.1M Magnesium chloride, ...Details: USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.0 mg/ml) AND RESERVOIR SOLUTION CONTAINING 24% v/v MPD, 0.1M Sodium acetate (pH 4.8), 0.1M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 30, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionRedundancy: 10.4 % / Av σ(I) over netI: 17.9 / Number: 333692 / Rmerge(I) obs: 0.097 / Χ2: 4.77 / D res high: 2.48 Å / D res low: 50 Å / Num. obs: 32052 / % possible obs: 78.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955099.910.0829.7269.5
3.934.9510010.0817.639.7
3.443.9310010.0926.2699.9
3.123.4410010.1114.8610.5
2.93.1210010.1333.4510.9
2.732.910010.1622.65311
2.592.7310010.1982.22611
2.482.5980.610.2241.90810.9
ReflectionResolution: 2.5→50 Å / Num. all: 31973 / Num. obs: 31973 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rsym value: 0.092 / Χ2: 1.174 / Net I/σ(I): 19
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5911.20.22131680.7721100
2.59-2.6911.30.19931601.0131100
2.69-2.8211.20.17432161.1971100
2.82-2.9611.20.14731761.531100
2.96-3.1510.90.12231801.0621100
3.15-3.3910.60.10632031.5961100
3.39-3.7310.20.09131821.0811100
3.73-4.27100.0832031.2621100
4.27-5.389.70.07532091.3541100
5.38-509.20.07132761.491199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
SGXPROphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→40.67 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3214 10 %Random
Rwork0.213 ---
obs-31920 99.8 %-
Solvent computationBsol: 23.899 Å2
Displacement parametersBiso mean: 38.998 Å2
Baniso -1Baniso -2Baniso -3
1-1.948 Å2-4.887 Å20 Å2
2--1.948 Å20 Å2
3----3.896 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 0 131 4019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.158
X-RAY DIFFRACTIONc_mcbond_it1.5941.5
X-RAY DIFFRACTIONc_scbond_it2.1682
X-RAY DIFFRACTIONc_mcangle_it2.7542
X-RAY DIFFRACTIONc_scangle_it3.2092.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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