[English] 日本語
Yorodumi
- PDB-6d9r: The substrate-bound crystal structure of HPRT (hypoxanthine phosp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d9r
TitleThe substrate-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase)
ComponentsHypoxanthine phosphoribosyltransferaseHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / HPRT / hypoxanthine phosphoribosyltransferase
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Hypoxanthine phosphoribosyltransferase / Hypoxanthine-guanine 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 / Phosphoribosyl pyrophosphate


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

-
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 / Diethylene glycol


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


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


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


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more