[English] 日本語
Yorodumi
- PDB-1qk3: TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qk3
TitleTOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE GMP COMPLEX
ComponentsHYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / PURINE SALVAGE
Function / homology
Function and homology information


xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / 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 / : / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Hypoxanthine-guanine-xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHeroux, A. / White, E.L. / Ross, L.J. / Borhani, D.W.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystal Structures of the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase Gmp and -Imp Complexes: Comparison of Purine Binding Interactions with the Xmp Complex
Authors: Heroux, A. / White, E.L. / Ross, L.J. / Borhani, D.W.
#1: Journal: Biochemistry / Year: 1999
Title: Crystal Structure of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two Mg2+ Ions Bound: Insights Into the Catalytic Mechanism
Authors: Heroux, A. / White, E.L. / Ross, L.J. / Davis, R.L. / Borhani, D.W.
#2: Journal: Gene / Year: 1994
Title: Isolation and Sequencing of a Cdna Encoding the Hypoxanthine-Guanine Phosphoribosyltransferase from Toxoplasma Gondii
Authors: Vasanthakumar, G. / Van Ginkel, S. / Parish, G.
History
DepositionJul 9, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
C: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
D: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2758
Polymers106,8224
Non-polymers1,4534
Water11,620645
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-28.1 kcal/mol
Surface area46910 Å2
MethodPQS
Unit cell
Length a, b, c (Å)65.453, 90.842, 80.256
Angle α, β, γ (deg.)90.00, 92.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.998952, 0.03121, 0.033478), (0.031671, -0.056695, 0.997889), (0.033042, 0.997904, 0.055647)144.944, -18.2291, 12.689
2given(0.634533, -0.598264, 0.489333), (-0.586699, -0.784988, -0.198945), (0.503142, -0.160854, -0.849102)26.5256, 211.8541, 165.66859
3given(-0.626453, 0.562888, -0.539178), (0.55054, -0.170149, -0.817285), (-0.55178, -0.80883, -0.203302)131.9211, 139.1158, 232.24879
DetailsTHE BIOMOLECULE CONSISTS OF A HOMO- TETRAMERIC COMPLEXOF BIOPOLYMERS

-
Components

#1: Protein
HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / HGPRTASE


Mass: 26705.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Plasmid: PETC1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q26997, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.09 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / pH: 5
Details: 15% PEG 8000, 100 MM KPO4 (PH 5-6), 0.25% BETA-OCTYLGLUCOPYRANOSIDE, 1 MM GMP, 277 K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 %PEG80001reservoir
2100 mMpotassium phosphate1reservoir
30.25 %octyl brta-D-glucopyranoside1reservoir
410-20 mg/mlprotein1drop
51 mMGMP1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 1996 / Details: RH MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.65→12.5 Å / Num. obs: 108535 / % possible obs: 96.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.053 / Net I/σ(I): 9.4
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.459 / % possible all: 85.3
Reflection
*PLUS
Num. measured all: 302104 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 85.3 % / Rmerge(I) obs: 0.459

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HMP, SUBUNIT A, WITHOUT LOOPS, WATERS, OR GMP

1hmp


Resolution: 1.65→12.5 Å / SU B: 1.27012 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11491 / ESU R Free: 0.10941
Details: THE STRUCTURE WAS FIRST REFINED USING X-XPLOR. REFMAC AND ARP WERE USED TO FINISH THE REFINEMENT, USING THE X-PLOR-CALCULATED BULK SOLVENT CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5403 5 %RANDOM
Rwork0.202 ---
obs-103103 96.4 %-
Displacement parametersBiso mean: 22.2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7197 0 96 645 7938
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6642
X-RAY DIFFRACTIONp_mcangle_it2.5783
X-RAY DIFFRACTIONp_scbond_it1.9752
X-RAY DIFFRACTIONp_scangle_it3.1323
X-RAY DIFFRACTIONp_plane_restr0.01040.02
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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