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- PDB-5esx: Crystal structure of hypoxanthine-guanine phosphoribosyltransfera... -

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Basic information

Entry
Database: PDB / ID: 5esx
TitleCrystal structure of hypoxanthine-guanine phosphoribosyltransferase complexed with GMP from Legionella pneumophila
ComponentsPurine/pyrimidine phosphoribosyltransferase
KeywordsTRANSFERASE / hypoxanthine-guanine phosphoribosyltransferase
Function / homologyRossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / GUANOSINE-5'-MONOPHOSPHATE / :
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.71 Å
AuthorsZhang, N. / Gong, X. / Lu, M. / Chen, X. / Qin, X. / Ge, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400641 China
National Natural Science Foundation of China31270770 China
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structures of Apo and GMP bound hypoxanthine-guanine phosphoribosyltransferase from Legionella pneumophila and the implications in gouty arthritis
Authors: Zhang, N. / Gong, X. / Lu, M. / Chen, X. / Qin, X. / Ge, H.
History
DepositionNov 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine/pyrimidine phosphoribosyltransferase
B: Purine/pyrimidine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4874
Polymers43,7602
Non-polymers7262
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-23 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.461, 67.538, 94.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Purine/pyrimidine phosphoribosyltransferase / hypoxanthine-guanine phosphoribosyltransferase


Mass: 21880.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Strain: ATCC 43290 / Gene: lp12_1457 / Production host: Escherichia coli (E. coli) / References: UniProt: G8UY25
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12269 / % possible obs: 99.9 % / Redundancy: 7.6 % / Net I/σ(I): 20.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.71→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24045 572 4.7 %RANDOM
Rwork0.18058 ---
obs0.18336 11650 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.096 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å20 Å2
2--2.62 Å2-0 Å2
3----6.07 Å2
Refinement stepCycle: LAST / Resolution: 2.71→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 48 26 2984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9854120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4524130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.71115497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7141516
X-RAY DIFFRACTIONr_chiral_restr0.1140.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212256
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0145.8121490
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.6578.7111859
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5746.0461534
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.60949.3014537
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.709→2.779 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 43 -
Rwork0.271 791 -
obs--95.86 %

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