[English] 日本語
Yorodumi
- PDB-2hmf: Structure of a Threonine Sensitive Aspartokinase from Methanococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hmf
TitleStructure of a Threonine Sensitive Aspartokinase from Methanococcus jannaschii Complexed with Mg-ADP and Aspartate
ComponentsProbable aspartokinase
KeywordsTRANSFERASE / Aspartokinase
Function / homology
Function and homology information


aspartate kinase / homoserine biosynthetic process / aspartate kinase activity / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / phosphorylation / ATP binding / cytosol
Similarity search - Function
Lysine-sensitive aspartokinase catalytic domain / VC0802-like / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / VC0802-like / ACT domain ...Lysine-sensitive aspartokinase catalytic domain / VC0802-like / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / VC0802-like / ACT domain / Carbamate kinase / Acetylglutamate kinase-like / ACT domain profile. / ACT domain / ACT-like domain / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ASPARTIC ACID / Probable aspartokinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFaehnle, C.R. / Viola, R.E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: The initial step in the archaeal aspartate biosynthetic pathway catalyzed by a monofunctional aspartokinase.
Authors: Faehnle, C.R. / Liu, X. / Pavlovsky, A. / Viola, R.E.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Probable aspartokinase
B: Probable aspartokinase
C: Probable aspartokinase
D: Probable aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,43316
Polymers204,0954
Non-polymers2,33812
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18470 Å2
ΔGint-133 kcal/mol
Surface area67620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.741, 104.508, 192.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 2 - 470 / Label seq-ID: 1 - 469

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
Probable aspartokinase / Aspartate kinase


Mass: 51023.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET 41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q57991, aspartate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5 800 mM ammonium formate 13% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 16, 2003
RadiationMonochromator: Diamond (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 18.4 / Number: 318472 / Rmerge(I) obs: 0.046 / Χ2: 1.04 / D res high: 2.5 Å / D res low: 30 Å / Num. obs: 60800 / % possible obs: 84.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.38309310.021.03
4.275.3896.510.0270.997
3.734.2797.710.0431.024
3.393.7398.310.0831.069
3.153.3998.810.090.957
2.963.1597.710.1371.088
2.822.9691.110.2051.078
2.692.8277.910.2481.114
2.592.6956.410.2361.109
2.52.593710.2771.129
ReflectionResolution: 2.5→50 Å / Num. all: 60800 / Num. obs: 60800 / % possible obs: 84.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.046 / Χ2: 1.04 / Net I/σ(I): 18.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.277 / Num. unique all: 2612 / Χ2: 1.129 / % possible all: 37

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CDQ

2cdq


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.888 / SU B: 16.234 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2727 5.1 %RANDOM
Rwork0.241 ---
obs0.243 53864 94.12 %-
all-60800 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.452 Å2
Baniso -1Baniso -2Baniso -3
1--3.17 Å20 Å20 Å2
2---0.96 Å20 Å2
3---4.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14160 0 148 123 14431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02214471
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.99619511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45351850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03724.786560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.294152745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2361588
X-RAY DIFFRACTIONr_chiral_restr0.0870.22334
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210360
X-RAY DIFFRACTIONr_nbd_refined0.2090.26700
X-RAY DIFFRACTIONr_nbtor_refined0.3030.29986
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2503
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.27
X-RAY DIFFRACTIONr_mcbond_it0.4721.59466
X-RAY DIFFRACTIONr_mcangle_it0.791214848
X-RAY DIFFRACTIONr_scbond_it0.94835554
X-RAY DIFFRACTIONr_scangle_it1.6654.54663
Refine LS restraints NCS

Ens-ID: 1 / Number: 3538 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.030.05
2BTIGHT POSITIONAL0.030.05
3CTIGHT POSITIONAL0.030.05
4DTIGHT POSITIONAL0.030.05
1ATIGHT THERMAL0.060.5
2BTIGHT THERMAL0.060.5
3CTIGHT THERMAL0.070.5
4DTIGHT THERMAL0.060.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 152 -
Rwork0.335 3004 -
obs-3156 75.99 %

+
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