[English] 日本語
Yorodumi
- PDB-1usy: ATP phosphoribosyl transferase (HisG:HisZ) complex from Thermotog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1usy
TitleATP phosphoribosyl transferase (HisG:HisZ) complex from Thermotoga maritima
Components
  • (ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY ...) x 2
  • (ATP PHOSPHORIBOSYLTRANSFERASE) x 2
KeywordsTRANSFERASE / ATP PHOSPHORIBOSYL TRANSFERASE / AMINOACYL-TRNA SYNTHETASE
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / L-histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase regulatory subunit / ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase ...ATP phosphoribosyltransferase regulatory subunit / ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / PHOSPHATE ION / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase regulatory subunit
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.52 Å
AuthorsVega, M.C. / Fernandez, F.J. / Murphy, G.E. / Zou, P. / Popov, A. / Wilmanns, M.
CitationJournal: Mol.Microbiol. / Year: 2005
Title: Regulation of the Hetero-Octameric ATP Phosphoribosyl Transferase Complex from Thermotoga Maritima by a tRNA Synthetase-Like Subunit.
Authors: Vega, M.C. / Zou, P. / Fernandez, F.J. / Murphy, G.E. / Sterner, R. / Popov, A. / Wilmanns, M.
History
DepositionDec 1, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 25, 2013Group: Atomic model / Derived calculations / Other
Revision 1.3Sep 10, 2014Group: Database references / Other
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY SUBUNIT
B: ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY SUBUNIT
C: ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY SUBUNIT
D: ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY SUBUNIT
E: ATP PHOSPHORIBOSYLTRANSFERASE
F: ATP PHOSPHORIBOSYLTRANSFERASE
G: ATP PHOSPHORIBOSYLTRANSFERASE
H: ATP PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,33122
Polymers219,5128
Non-polymers1,81914
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25400 Å2
ΔGint-165.7 kcal/mol
Surface area79810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.580, 134.403, 154.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY ... , 2 types, 4 molecules ABDC

#1: Protein ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY SUBUNIT


Mass: 31326.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9X0D3
#2: Protein ATP PHOSPHORIBOSYLTRANSFERASE REGULATORY SUBUNIT


Mass: 31354.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9X0D3

-
Protein , 2 types, 4 molecules EFGH

#3: Protein ATP PHOSPHORIBOSYLTRANSFERASE


Mass: 23544.416 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9X0D2, ATP phosphoribosyltransferase
#4: Protein ATP PHOSPHORIBOSYLTRANSFERASE


Mass: 23544.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9X0D2, ATP phosphoribosyltransferase

-
Non-polymers , 3 types, 288 molecules

#5: Chemical
ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H10N3O2
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.44 Å3/Da / Density % sol: 49.2 %
Crystal growpH: 4.2 / Details: pH 4.20

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9788
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2002 / Details: COLLIMATOR
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 52743 / % possible obs: 98.4 % / Redundancy: 17.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.44
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 6.86 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.52→12 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.84 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.05 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.287 3524 5.1 %RANDOM
Rwork0.203 ---
obs0.207 66055 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.52→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15244 0 118 274 15636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02215548
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.97720972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96151893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.22386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211476
X-RAY DIFFRACTIONr_gen_planes_other0.2850.021
X-RAY DIFFRACTIONr_nbd_refined0.2730.27248
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2626
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.41759492
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.165615429
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.37766056
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.4027.55543
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
LS refinement shellResolution: 2.52→2.58 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.393 249
Rwork0.27 4322
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.54751.35060.54291.8653-0.11391.2213-0.13470.0109-0.3846-0.13240.1352-0.11370.12190.1292-0.00060.16350.05370.02620.16810.05580.1022-9.881931.1545-14.7761
23.39671.7937-0.09492.08490.4680.9184-0.07560.19830.3679-0.22570.06280.1264-0.1547-0.18250.01280.18530.0682-0.05280.1467-0.00180.165313.896567.4947-12.9059
32.2225-0.9138-0.31981.9868-0.47011.2795-0.0336-0.29460.19750.22140.0523-0.0959-0.15370.1422-0.01870.1735-0.04420.00820.1397-0.00190.0264-3.589263.9379-66.4752
43.2978-1.63690.69553.30360.45180.83520.041-0.1538-0.29440.14280.15650.08460.1748-0.0844-0.19750.236-0.0368-0.01950.20050.03870.054819.501627.5315-59.5549
51.958-0.1275-0.74451.67151.20567.12090.11020.043-0.09620.14410.0117-0.19620.14870.1629-0.12190.1514-0.0191-0.04440.0797-0.07120.209639.415936.1409-38.6751
60.88640.29950.51061.5288-0.4357.4835-0.06-0.00990.05930.17890.00480.0129-0.2248-0.23670.05530.14320.02320.03710.07070.03480.2384-28.394359.2379-48.6572
72.05280.1453-1.50361.4237-0.06476.932-0.11070.0385-0.0721-0.1820.02450.06760.0758-0.10440.08610.0701-0.0072-0.04080.00710.03730.1961-29.67536.6608-36.9507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION2B1 - 275
3X-RAY DIFFRACTION3C1 - 275
4X-RAY DIFFRACTION4D1 - 275
5X-RAY DIFFRACTION5F1 - 203
6X-RAY DIFFRACTION6G1 - 203
7X-RAY DIFFRACTION7H1 - 201

+
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://pdbjlvh1.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