[English] 日本語
Yorodumi
- PDB-3s1t: Structure of the regulatory domain of aspartokinase (Rv3709c; AK-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s1t
TitleStructure of the regulatory domain of aspartokinase (Rv3709c; AK-beta) in complex with threonine from Mycobacterium tuberculosis
Components(Aspartokinase) x 2
KeywordsTRANSFERASE / ACT domain / Threonine binding / regulatory domain of aspartokinase
Function / homology
Function and homology information


aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / peptidoglycan-based cell wall / phosphorylation / ATP binding / plasma membrane / cytosol
Similarity search - Function
Aspartokinase catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / ACT domain / ACT domain / ACT domain profile. ...Aspartokinase catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / ACT domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THREONINE / Aspartokinase / Aspartokinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSchuldt, L. / Mueller-Dieckmann, J. / Weiss, M.S.
Citation
Journal: To be Published
Title: High-resolution X-ray structure of the regulatory domain of the mycobacterial aspartokinase in complex with threonine
Authors: Schuldt, L. / Mueller-Dieckmann, J. / Weiss, M.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the regulatory domain of aspartokinase (Rv3709c) from Mycobacterium tuberculosis
Authors: Schuldt, L. / Suchowersky, R. / Veith, K. / Mueller-Dieckmann, J. / Weiss, M.S.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Database references / Derived calculations
Category: diffrn_source / pdbx_struct_assembly ...diffrn_source / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.value / _struct_ref_seq_dif.details
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Aspartokinase
B: Aspartokinase
C: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,77912
Polymers39,8683
Non-polymers9119
Water3,945219
1
A: Aspartokinase
B: Aspartokinase
hetero molecules

C: Aspartokinase


Theoretical massNumber of molelcules
Total (without water)40,77912
Polymers39,8683
Non-polymers9119
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area6310 Å2
ΔGint-99 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.700, 63.430, 108.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Aspartokinase / Aspartate kinase / ASK


Mass: 19364.801 Da / Num. of mol.: 2 / Fragment: Aspartokinase beta-subunit, residues 251-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ask, MT3812, MTV025.057c, Rv3709c / Plasmid: pETM-13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) cc2
References: UniProt: P0A4Z8, UniProt: P9WPX3*PLUS, aspartate kinase
#2: Protein/peptide Aspartokinase


Mass: 1138.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: pETM-13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) cc2 / References: UniProt: P0A4Z8, UniProt: P9WPX3*PLUS
#3: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAUTHORS STATE THAT THE ASYMMETRIC UNIT OF THE CRYSTALS CONTAINS A HOMODIMER FORMED BY THE TWO ...AUTHORS STATE THAT THE ASYMMETRIC UNIT OF THE CRYSTALS CONTAINS A HOMODIMER FORMED BY THE TWO POLYPEPTIDE CHAINS A AND B (SEQUENCE RANGE 3-160). CHAIN C REPRESENTS THE C-TERMINAL TAIL OF THE POLYPEPTIDE CHAIN (SEQUENCE RANGE 163-173). DUE TO LACK OF ELECTRON DENSITY IN THE LINKER REGION, IT COULD NOT BE UNAMBIGUOUSLY ASSIGNED WHEATHER THIS FRAGMENT ORIGINATES FROM CHAIN A OR FROM CHAIN B OF A NEIGHBORING ASYMMETRIC UNIT. HENCE THE FRAGMENT WAS DECLARED AS CHAIN C. THIS IS ALSO DISCUSSED IN THE PUBLICATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: ammonium sulphate, bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→99 Å / Num. all: 48122 / Num. obs: 47641 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.63→1.65 Å / % possible all: 100

-
Processing

SoftwareName: REFMAC / Version: 5.6.0091 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DTJ

2dtj


Resolution: 1.63→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.197 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21143 1450 3.1 %RANDOM
Rwork0.19258 ---
all0.19318 47148 --
obs0.19318 45214 98.95 %-
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: 23.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å20 Å2
2---0.2 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.63→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 51 219 2679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222522
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9893437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.35624.64699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68915422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0151515
X-RAY DIFFRACTIONr_chiral_restr0.1180.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211841
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 109 -
Rwork0.287 3098 -
obs--99.97 %
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)
18.56832.3167-7.47783.9301-5.268419.8820.28210.05520.25030.37040.0210.0643-0.46980.0014-0.30310.10770.0107-0.03440.0054-0.01450.063132.718541.285529.4167
24.25420.0182-0.55040.56480.37951.6372-0.01070.0940.0036-0.0233-0.0013-0.06260.09720.0380.01190.0199-0.0058-0.00390.05070.01120.039124.161344.50063.6961
31.0907-0.92760.29373.0701-0.72372.9006-0.1222-0.0303-0.14810.22960.11150.13870.048-0.16260.01060.0866-0.0109-0.01840.0443-0.0060.053126.62347.809726.9824
45.77661.05220.34841.8154-0.01858.0388-0.01640.0215-0.05120.29920.1493-0.2984-0.09690.4569-0.13290.07450.0233-0.04280.04-0.03180.080535.568148.763426.45
513.0439-13.406514.560615.312-14.343516.5579-0.56350.2630.5290.2249-0.0828-0.0664-0.74520.50050.64630.1507-0.0728-0.02080.4062-0.05960.409953.190524.788838.5691
618.7666-15.7919-5.471322.01996.96494.25920.43710.5918-0.402-0.0924-0.46780.16420.3715-0.36370.03070.2748-0.0465-0.02780.08530.03810.062214.038628.612718.018
73.02150.76850.20232.7850.74311.2393-0.03070.0330.14150.16030.0210.1975-0.0688-0.20070.00970.10290.01810.00670.06180.00760.058714.793755.295423.1079
80.2213-0.19-0.79434.74190.06512.9417-0.1127-0.0553-0.01030.22170.028-0.38280.41850.17730.08470.1255-0.0311-0.03510.0920.02360.097316.681834.744611.7683
94.3532-2.28320.02368.00662.64182.86670.0544-0.0246-0.33080.4186-0.25240.5480.6767-0.55130.1980.1941-0.1190.03930.17190.0170.09198.302732.89413.1272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 13
2X-RAY DIFFRACTION2A14 - 94
3X-RAY DIFFRACTION3A95 - 134
4X-RAY DIFFRACTION4A135 - 160
5X-RAY DIFFRACTION5C163 - 173
6X-RAY DIFFRACTION6B3 - 13
7X-RAY DIFFRACTION7B14 - 94
8X-RAY DIFFRACTION8B95 - 134
9X-RAY DIFFRACTION9B135 - 158

+
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