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- PDB-2p8t: Hypothetical protein PH0730 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2p8t
TitleHypothetical protein PH0730 from Pyrococcus horikoshii OT3
ComponentsHypothetical protein PH0730Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PH0730 / 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


aminoacyl-tRNA ligase activity / translation / ATP binding / cytoplasm
Similarity search - Function
Domain of unknown function DUF4443 / Domain of unknown function (DUF4443) / GAD-like domain / GAD-like domain superfamily / Gyrase A; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich ...Domain of unknown function DUF4443 / Domain of unknown function (DUF4443) / GAD-like domain / GAD-like domain superfamily / Gyrase A; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DUF4443 domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChen, L. / Zhao, M. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhu, J. / Swindell, J.T. / Fu, Z.-Q. / Chrzas, J. ...Chen, L. / Zhao, M. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhu, J. / Swindell, J.T. / Fu, Z.-Q. / 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: Hypothetical protein PH0730 from Pyrococcus horikoshii OT3
Authors: Chen, L. / Zhao, M. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhu, J. / Swindell, J.T. / Fu, Z.-Q. / Chrzas, J. / Rose, J.P. / Wang, B.-C.
History
DepositionMar 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 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 1.3Sep 13, 2017Group: Refinement description / Category: refine / software
Item: _refine.pdbx_method_to_determine_struct / _software.classification ..._refine.pdbx_method_to_determine_struct / _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 1.5Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein PH0730


Theoretical massNumber of molelcules
Total (without water)22,6641
Polymers22,6641
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.709, 60.971, 84.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein Hypothetical protein PH0730 / Hypothesis


Mass: 22663.584 Da / Num. of mol.: 1 / Mutation: MLLKVYLALKQRKI at N-terminal have been truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0730 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: O58461
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (7.8 mg/ml) AND RESERVOIR SOLUTION CONTAINING 30% w/v PEG4000, 0.2M Mg chloride, 0.1M Tris-HCl (pH 8.4) , VAPOR ...Details: USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (7.8 mg/ml) AND RESERVOIR SOLUTION CONTAINING 30% w/v PEG4000, 0.2M Mg chloride, 0.1M Tris-HCl (pH 8.4) , 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: 0.97243 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 31, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionRedundancy: 13.1 % / Av σ(I) over netI: 17.7 / Number: 223902 / Rmerge(I) obs: 0.079 / Χ2: 2.56 / D res high: 1.79 Å / D res low: 50 Å / Num. obs: 17130 / % possible obs: 96.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.865099.510.0652.55612.7
3.063.8610010.0733.10613.7
2.673.0610010.083.64113.9
2.432.6710010.0963.26514
2.262.4310010.1052.94314
2.122.2610010.1222.38214.2
2.022.1299.810.1462.01513.8
1.932.0299.210.1841.70712.7
1.851.9393.410.211.54311.4
1.791.8576.910.241.4559.3
ReflectionResolution: 1.79→50 Å / Num. all: 17130 / Num. obs: 17130 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rsym value: 0.079 / Χ2: 2.558 / Net I/σ(I): 17.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.859.30.2413311.455176.9
1.85-1.9311.40.2116281.543193.4
1.93-2.0212.70.18417011.707199.2
2.02-2.1213.80.14617322.015199.8
2.12-2.2614.20.12217292.3821100
2.26-2.43140.10517592.9431100
2.43-2.67140.09617803.2651100
2.67-3.0613.90.0817673.6411100
3.06-3.8613.70.07317983.1061100
3.86-5012.70.06519052.556199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
ISASPIPELINEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.459 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 852 5 %RANDOM
Rwork0.227 ---
obs0.229 16882 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.451 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å20 Å2
2--3.1 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 0 117 1580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221488
X-RAY DIFFRACTIONr_angle_refined_deg1.2382.0072007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29924.57659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89215292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.597158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021065
X-RAY DIFFRACTIONr_nbd_refined0.2110.2752
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.29
X-RAY DIFFRACTIONr_mcbond_it0.9241.5951
X-RAY DIFFRACTIONr_mcangle_it1.51521496
X-RAY DIFFRACTIONr_scbond_it2.323597
X-RAY DIFFRACTIONr_scangle_it3.6994.5511
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 57 -
Rwork0.255 980 -
obs-1037 82.83 %

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