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- PDB-3ohp: Crystal structure of HGPRT from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 3ohp
TitleCrystal structure of HGPRT from Vibrio cholerae
ComponentsHypoxanthine phosphoribosyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / phosphoribosyltransferase
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsKim, J. / Ramagopal, U.A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of HGPRT from Vibrio cholerae
Authors: Kim, J. / Ramagopal, U.A. / Almo, S.C. / Burley, S.K.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Other
Revision 1.3Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
C: Hypoxanthine phosphoribosyltransferase
D: Hypoxanthine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)80,5404
Polymers80,5404
Non-polymers00
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-38 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.511, 145.213, 51.611
Angle α, β, γ (deg.)90.00, 94.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypoxanthine phosphoribosyltransferase


Mass: 20135.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: hpt, VC_0585 / Plasmid: LIC-PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9KUD7, hypoxanthine phosphoribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M citrate PH 5.5, 20% PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2010
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 47025 / Num. obs: 46597 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.058 / Net I/σ(I): 17.8
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4386 / Rsym value: 0.294 / % possible all: 92.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP10.2.23phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G9S

1g9s


Resolution: 2.04→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.576 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22421 2360 5.1 %RANDOM
Rwork0.18015 ---
obs0.18235 44269 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.106 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20.74 Å2
2---1.64 Å20 Å2
3---2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.04→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 0 269 5592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225448
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9717373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16724.186258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.789151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4041545
X-RAY DIFFRACTIONr_chiral_restr0.1010.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214025
X-RAY DIFFRACTIONr_mcbond_it0.7551.53342
X-RAY DIFFRACTIONr_mcangle_it1.40525451
X-RAY DIFFRACTIONr_scbond_it2.38632106
X-RAY DIFFRACTIONr_scangle_it3.8054.51922
LS refinement shellResolution: 2.038→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 193 -
Rwork0.218 3128 -
obs--94.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19460.3315-0.11621.521-0.0340.5937-0.01970.0733-0.0034-0.01440.009-0.0617-0.00010.01970.01070.0333-0.0006-0.00420.05960.01180.005711.2460.4311.673
21.501-0.2547-0.01391.3095-0.30750.5160.0024-0.08930.04840.0826-0.00470.0961-0.01740.02990.00230.0382-0.01160.00680.0398-0.0070.0126-9.942.6638.629
30.9246-0.5436-0.00512.8318-0.05790.7654-0.0531-0.07680.0310.15520.0033-0.17670.03750.0280.04980.01430.00780.00540.03240.02690.070310.93938.291-0.195
41.14790.2117-0.28842.7596-0.54180.79450.00310.1225-0.0362-0.21580.00130.45150.0378-0.0108-0.00440.01790.0057-0.03270.03270.01440.1072-8.76835.809-10.103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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