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- PDB-2phc: Crystal structure of conserved uncharacterized protein PH0987 fro... -

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Basic information

Entry
Database: PDB / ID: 2phc
TitleCrystal structure of conserved uncharacterized protein PH0987 from Pyrococcus horikoshii
ComponentsUncharacterized protein PH0987
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PH0730 / Pyrococcus horikoshii / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / PSI / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


hydrolase activity / ATP binding
Similarity search - Function
KipI family / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gyrase A; domain 2 - #40 / Cyclophilin-like / Cyclophilin / Cyclophilin-like domain superfamily / Gyrase A; domain 2 / Beta Barrel ...KipI family / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gyrase A; domain 2 - #40 / Cyclophilin-like / Cyclophilin / Cyclophilin-like domain superfamily / Gyrase A; domain 2 / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AHS1 domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.29 Å
AuthorsSwindell II, J.T. / Chen, L. / Zhu, J. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Chrzas, J. / Rose, J.P. ...Swindell II, J.T. / Chen, L. / Zhu, J. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / 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: Crystal structure of conserved uncharacterized protein PH0987 from Pyrococcus horikoshii.
Authors: Swindell II, J.T. / Chen, L. / Zhu, J. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Fu, Z.-Q. / Chrzas, J. / Rose, J.P. / Wang, B.-C.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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
B: Uncharacterized protein PH0987


Theoretical massNumber of molelcules
Total (without water)25,3241
Polymers25,3241
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.848, 105.848, 51.869
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe biological assembly is a monomer

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Components

#1: Protein Uncharacterized protein PH0987


Mass: 25323.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0987 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: O58715
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.23 mg/mL) IN 20mM Tris-HCl pH 8.0, 1mM DTT, AND SOLUTION CONTAINING 17.5% w/v PEG 3350, 0.2 M Na Iodide, VAPOR ...Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.23 mg/mL) IN 20mM Tris-HCl pH 8.0, 1mM DTT, AND SOLUTION CONTAINING 17.5% w/v PEG 3350, 0.2 M Na Iodide, VAPOR DIFFUSION, temperature 289K

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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
ReflectionResolution: 2.29→50 Å / Num. obs: 15078 / % possible obs: 100 % / Redundancy: 15 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 28.1
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.322 / Num. unique all: 1499 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se37.6470.8930.3420.0220.719
2Se55.8710.6840.1280.960.584

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.29→18.33 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.865 / SU B: 6.546 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 761 5.1 %RANDOM
Rwork0.239 ---
obs0.242 15018 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.324 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.29→18.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 0 91 1781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221737
X-RAY DIFFRACTIONr_angle_refined_deg2.5811.9832362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg22.8085215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36523.09971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9815275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3811511
X-RAY DIFFRACTIONr_chiral_restr0.2320.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021329
X-RAY DIFFRACTIONr_nbd_refined0.2450.2711
X-RAY DIFFRACTIONr_nbtor_refined0.3280.21140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3060.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.210
X-RAY DIFFRACTIONr_mcbond_it2.1021.51120
X-RAY DIFFRACTIONr_mcangle_it2.34321745
X-RAY DIFFRACTIONr_scbond_it4.0923741
X-RAY DIFFRACTIONr_scangle_it5.5514.5617
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 52 -
Rwork0.265 1067 -
obs-1119 99.64 %

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