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- PDB-1v30: Crystal Structure Of Uncharacterized Protein PH0828 From Pyrococc... -

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Basic information

Entry
Database: PDB / ID: 1v30
TitleCrystal Structure Of Uncharacterized Protein PH0828 From Pyrococcus horikoshii
ComponentsHypothetical UPF0131 protein PH0828
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA+BETA
Function / homology
Function and homology information


Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity
Similarity search - Function
Gamma-glutamylcyclotransferase, AIG2-like domain / Gamma-glutamyl cyclotransferase, AIG2-like / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Putative gamma-glutamylcyclotransferase PH0828
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTajika, Y. / Sakai, N. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of hypothetical protein PH0828 from Pyrococcus horikoshii.
Authors: Tajika, Y. / Sakai, N. / Tamura, T. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionOct 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical UPF0131 protein PH0828
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9712
Polymers14,7641
Non-polymers2071
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.692, 51.692, 81.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypothetical UPF0131 protein PH0828


Mass: 14763.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O58558
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: Sodium Citrate , pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→17.3 Å / Num. obs: 25279 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 25.97 Å2 / Rsym value: 0.084 / Net I/σ(I): 3.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.28 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
SHARPphasing
CNSrefinement
HKL-2000data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→7 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2492 9.9 %RANDOM
Rwork0.217 ---
obs0.217 25014 99.4 %-
all-25014 --
Solvent computationSolvent model: THROUGHOUT
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å2-0.56 Å20 Å2
2---2.36 Å20 Å2
3---4.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.4→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms995 0 13 181 1189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.61
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.098
X-RAY DIFFRACTIONc_mcangle_it1.656
X-RAY DIFFRACTIONc_scbond_it1.884
X-RAY DIFFRACTIONc_scangle_it2.787
LS refinement shellResolution: 1.4→1.45 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.286 249 10.17 %
Rwork0.261 2199 -
obs-2448 100 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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