[English] 日本語
Yorodumi
- PDB-1kmm: HISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDYL-ADENYLATE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kmm
TitleHISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDYL-ADENYLATE
ComponentsHISTIDYL-TRNA SYNTHETASE
KeywordsAMINOACYL-TRNA SYNTHASE / LIGASE / SYNTHETASE
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Histidyl-anticodon-binding / Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily ...Histidyl-anticodon-binding / Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDYL-ADENOSINE MONOPHOSPHATE / Histidine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsArnez, J.G. / Francklyn, C.S. / Moras, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase.
Authors: Arnez, J.G. / Augustine, J.G. / Moras, D. / Francklyn, C.S.
#1: Journal: Embo J. / Year: 1995
Title: Crystal Structure of Histidyl-tRNA Synthetase from Escherichia Coli Complexed with Histidyl-Adenylate
Authors: Arnez, J.G. / Harris, D.C. / Mitschler, A. / Rees, B. / Francklyn, C.S. / Moras, D.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of Histidyl-tRNA Synthetase from Escherichia Coli
Authors: Francklyn, C. / Harris, D. / Moras, D.
#3: Journal: J.Biol.Chem. / Year: 1985
Title: Primary Structure of Histidine-tRNA Synthetase and Characterization of Hiss Transcripts
Authors: Freedman, R. / Gibson, B. / Donovan, D. / Biemann, K. / Eisenbeis, S. / Parker, J. / Schimmel, P.
History
DepositionMay 9, 1997Processing site: BNL
Revision 1.0Dec 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: HISTIDYL-TRNA SYNTHETASE
B: HISTIDYL-TRNA SYNTHETASE
C: HISTIDYL-TRNA SYNTHETASE
D: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,2798
Polymers188,3414
Non-polymers1,9374
Water3,315184
1
A: HISTIDYL-TRNA SYNTHETASE
B: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1394
Polymers94,1712
Non-polymers9692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-25 kcal/mol
Surface area29290 Å2
MethodPISA
2
C: HISTIDYL-TRNA SYNTHETASE
D: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1394
Polymers94,1712
Non-polymers9692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-18 kcal/mol
Surface area29000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.400, 110.700, 108.700
Angle α, β, γ (deg.)115.00, 97.40, 90.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.218899, -0.011669, -0.975678), (-0.01932, -0.999681, 0.01629), (-0.975556, 0.022416, 0.218603)2.14363, 8.49779, 1.41208
2given(-0.999923, 0.008088, 0.009432), (0.008086, 0.999967, -0.000301), (-0.009434, -0.000225, -0.999956)-0.32185, -9.02249, -0.08287
3given(0.204406, 0.015114, 0.97877), (-0.018332, -0.999646, 0.019265), (0.978715, -0.02188, -0.204056)-2.48453, -0.7126, -1.78459

-
Components

#1: Protein
HISTIDYL-TRNA SYNTHETASE / HISTIDINE-TRNA LIGASE


Mass: 47085.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Description: INDUCTION WITH IPTG / Plasmid: PHRS-7 / Gene (production host): HISS / Production host: Escherichia coli (E. coli) / Variant (production host): TRP-LAC / References: UniProt: P60906, histidine-tRNA ligase
#2: Chemical
ChemComp-HAM / HISTIDYL-ADENOSINE MONOPHOSPHATE


Mass: 484.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H21N8O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.4 Å3/Da / Density % sol: 68 %
Description: MERGED DATA SET DATA SCALING SOFTWARE : MARSCALE
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.07-0.1 Menzyme1drop
350 mMhistidine1drop
43 mMATP1drop
50.1 Mcitrate1reservoir
60.2 Mammonium acetate1reservoir
730 %(w/v)PEG40001reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12751
22751
32751
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODESIEMENS11.5418
SYNCHROTRONLURE DW3220.94
SYNCHROTRONLURE DW3230.94
Detector
TypeIDDetectorDate
MAR scanner 180 mm plate1IMAGE PLATEFeb 9, 1994
MAR scanner 180 mm plate2IMAGE PLATEMar 22, 1994
MAR scanner 300 mm plate3IMAGE PLATENov 2, 1995
Radiation
IDMonochromatorMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITE (HUBER FLAT MONOCHROMATOR #151)Mx-ray1
2GRAPHITE (HUBER FLAT MONOCHROMATOR #151)Mx-ray2
3GRAPHITE (HUBER FLAT MONOCHROMATOR #151)Mx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.941
31
ReflectionResolution: 2.6→12 Å / Num. obs: 66471 / % possible obs: 85.4 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 69.7 Å2 / Rmerge(I) obs: 0.0956 / Net I/σ(I): 24
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4 / % possible all: 47.5
Reflection
*PLUS
Num. measured all: 183629
Reflection shell
*PLUS
% possible obs: 47.5 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MARXDSdata reduction
MARSCALEdata scaling
X-PLORphasing
RefinementResolution: 2.6→12 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.297 -2.5 %
Rwork0.221 --
obs0.221 52794 68 %
Displacement parametersBiso mean: 46.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11628 0 132 184 11944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.705
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.362 56 2.5 %
Rwork0.353 2105 -
obs--22 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.38
LS refinement shell
*PLUS
Rfactor obs: 0.353

+
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