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- PDB-5esw: Crystal structure of Apo hypoxanthine-guanine phosphoribosyltrans... -

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Basic information

Entry
Database: PDB / ID: 5esw
TitleCrystal structure of Apo hypoxanthine-guanine phosphoribosyltransferase from Legionella pneumophila
ComponentsPurine/pyrimidine phosphoribosyltransferase
KeywordsTRANSFERASE / hypoxanthine-guanine phosphoribosyltransferase
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / nucleotide binding / magnesium ion binding / cytosol
Similarity search - Function
: / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Purine/pyrimidine phosphoribosyltransferase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila strain Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,2323
Polymers44,1372
Non-polymers951
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-26 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.020, 67.892, 94.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 0 - 187 / Label seq-ID: 8 - 195

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 22068.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila strain Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg1519 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5ZVC1, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
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: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 17207 / % possible obs: 99.7 % / Redundancy: 7.1 % / Net I/σ(I): 17.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 7.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HGX

1hgx


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21885 869 5.1 %RANDOM
Rwork0.16532 ---
obs0.16782 16293 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.604 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å20 Å2-0 Å2
2--0.79 Å20 Å2
3----3.67 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 5 97 3072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193043
X-RAY DIFFRACTIONr_bond_other_d00.022960
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9674135
X-RAY DIFFRACTIONr_angle_other_deg3.58136798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86623.852135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19615515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1821518
X-RAY DIFFRACTIONr_chiral_restr0.1070.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213410
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02674
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10878 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 69 -
Rwork0.189 1141 -
obs--96.88 %

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