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- PDB-6d9r: The substrate-bound crystal structure of HPRT (hypoxanthine phosp... -

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Basic information

Entry
Database: PDB / ID: 6d9r
TitleThe substrate-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase)
ComponentsHypoxanthine phosphoribosyltransferase
KeywordsTRANSFERASE / HPRT / hypoxanthine 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 ...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 / metal ion binding / cytoplasm / 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
9-DEAZAGUANINE / ACETATE ION / DI(HYDROXYETHYL)ETHER / Chem-PRP / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsSatyshur, K.A. / Wolak, C. / Anderson, B. / Dubiel, K. / Keck, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM084003 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM07215 United States
National Science Foundation (NSF, United States)DGE-1256259 United States
CitationJournal: Elife / Year: 2019
Title: Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction.
Authors: Anderson, B.W. / Liu, K. / Wolak, C. / Dubiel, K. / She, F. / Satyshur, K.A. / Keck, J.L. / Wang, J.D.
History
DepositionApr 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,57529
Polymers41,0072
Non-polymers2,56827
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Also validated by cross-linking and dynamic light scattering.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-44 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.758, 113.758, 56.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

21B-392-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Hypoxanthine phosphoribosyltransferase / HPRT


Mass: 20503.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium)
Gene: hpt, hprT, hpt1, tilS, BA_0063, A9486_05730, ABW01_27435, BASH2_00187, BVG01_28865, CN272_24955, CN488_12230, CN504_22375, COE56_22980, COJ30_24475, COK92_19380, COL95_25280, MCCC1A01412_27610
Plasmid: pLIC trPC-HA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1S0QLD4, UniProt: B9ZW32*PLUS, hypoxanthine phosphoribosyltransferase
#3: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 342 molecules

#2: Chemical ChemComp-9DG / 9-DEAZAGUANINE


Mass: 150.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N4O
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, pH 4.6, 30% PEG4000
PH range: 4.6 - 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 8, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.64→40.167 Å / Num. obs: 51750 / % possible obs: 99.8 % / Redundancy: 21.5 % / Biso Wilson estimate: 19.34 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.137 / Net I/σ(I): 31.09
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 14.4 % / Num. unique obs: 2548 / CC1/2: 0.81 / Rpim(I) all: 0.35 / Rrim(I) all: 1.376 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
ADSCdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6D9S

6d9s


Resolution: 1.64→37.19 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.44
RfactorNum. reflection% reflection
Rfree0.1962 1994 3.85 %
Rwork0.1656 --
obs0.1668 51720 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2730 0 161 317 3208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013082
X-RAY DIFFRACTIONf_angle_d1.2234157
X-RAY DIFFRACTIONf_dihedral_angle_d16.1411884
X-RAY DIFFRACTIONf_chiral_restr0.063487
X-RAY DIFFRACTIONf_plane_restr0.008498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6397-1.68070.28221340.24043385X-RAY DIFFRACTION96
1.6807-1.72610.25221420.23033506X-RAY DIFFRACTION99
1.7261-1.77690.24121430.21893530X-RAY DIFFRACTION100
1.7769-1.83420.22711420.20783527X-RAY DIFFRACTION100
1.8342-1.89980.2531410.20373525X-RAY DIFFRACTION100
1.8998-1.97590.21341410.18593528X-RAY DIFFRACTION100
1.9759-2.06580.24331440.18673548X-RAY DIFFRACTION100
2.0658-2.17470.20631390.17553556X-RAY DIFFRACTION100
2.1747-2.31090.22011420.17183562X-RAY DIFFRACTION100
2.3109-2.48930.20191390.16813573X-RAY DIFFRACTION100
2.4893-2.73980.19631440.16163570X-RAY DIFFRACTION100
2.7398-3.13610.17141430.15923598X-RAY DIFFRACTION100
3.1361-3.95060.17571480.13853611X-RAY DIFFRACTION100
3.9506-40.17910.16591520.14553714X-RAY DIFFRACTION100

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