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- PDB-3bs4: Crystal structure of uncharacterized protein PH0321 from Pyrococc... -

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Basic information

Entry
Database: PDB / ID: 3bs4
TitleCrystal structure of uncharacterized protein PH0321 from Pyrococcus horikoshii in complex with an unknown peptide
Components
  • Uncharacterized protein PH0321
  • Unknown peptide
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyP-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / KaiC-like domain-containing protein
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Hu, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein PH0321 from Pyrococcus horikoshii in complex with an unknown peptide.
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Hu, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: Uncharacterized protein PH0321
B: Unknown peptide


Theoretical massNumber of molelcules
Total (without water)30,9322
Polymers30,9322
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.241, 71.121, 49.581
Angle α, β, γ (deg.)90.000, 93.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-393-

HOH

DetailsAUTHORS STATE THAT THE ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein Uncharacterized protein PH0321


Mass: 30539.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0321 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58059
#2: Protein/peptide Unknown peptide


Mass: 392.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Unknown peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 100mM Tri-sodium citrate dihydrate pH 7.0, 20% PEG 4000, 20% Isopropanol, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2007
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.6→57.378 Å / Num. all: 43226 / Num. obs: 43226 / % possible obs: 97.17 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6216 / Rsym value: 0.669 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.426 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2179 5 %RANDOM
Rwork0.184 ---
obs0.185 43223 97.17 %-
all-43223 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20.81 Å2
2--0.02 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 192 2246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222146
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9722896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2175258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19222.52599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77515409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2661518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021594
X-RAY DIFFRACTIONr_nbd_refined0.2010.2913
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2177
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.218
X-RAY DIFFRACTIONr_mcbond_it0.8951.51286
X-RAY DIFFRACTIONr_mcangle_it1.45722021
X-RAY DIFFRACTIONr_scbond_it2.4113996
X-RAY DIFFRACTIONr_scangle_it3.8134.5868
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 147 -
Rwork0.227 2964 -
all-3111 -
obs-2964 96.17 %

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