[English] 日本語
Yorodumi
- PDB-1n8w: Biochemical and Structural Studies of Malate Synthase from Mycoba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n8w
TitleBiochemical and Structural Studies of Malate Synthase from Mycobacterium tuberculosis
ComponentsProbable malate synthase G
KeywordsLYASE / MALATE SYNTHASE / GLYOXYLATE PATHWAY / MYCOBACTERIUM TUBERCULOSIS / MALATE / COENZYME A / GLCB / GLYOXYLATE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate catabolic process / glyoxylate cycle / fibronectin binding ...host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate catabolic process / glyoxylate cycle / fibronectin binding / laminin binding / tricarboxylic acid cycle / peptidoglycan-based cell wall / manganese ion binding / magnesium ion binding / cell surface / protein homodimerization activity / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Malate synthase G - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / : / Malate synthase G, alpha-beta insertion domain / : / : / Malate synthase, N-terminal domain / Malate synthase, C-terminal / Malate synthase G / Malate synthase, domain III ...Malate synthase G - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / : / Malate synthase G, alpha-beta insertion domain / : / : / Malate synthase, N-terminal domain / Malate synthase, C-terminal / Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate synthase, N-terminal and TIM-barrel domains / Malate Synthase G; Chain: A; Domain 4 / Malate synthase, C-terminal superfamily / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain / Beta Complex / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A / GLYOXYLIC ACID / D-MALATE / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSmith, C.V. / Huang, C.C. / Miczak, A. / Russell, D.G. / Sacchettini, J.C. / Honer zu Bentrup, K. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Biochemical and structural studies of malate synthase from Mycobacterium tuberculosis
Authors: Smith, C.V. / Huang, C.C. / Miczak, A. / Russell, D.G. / Sacchettini, J.C. / Honer Zu Bentrup, K.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 malate synthase G
B: Probable malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,55812
Polymers160,9782
Non-polymers1,58110
Water11,512639
1
A: Probable malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7417
Polymers80,4891
Non-polymers1,2526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8175
Polymers80,4891
Non-polymers3284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.985, 120.985, 232.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Probable malate synthase G


Mass: 80488.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: GlcB / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A5J4, UniProt: P9WK17*PLUS, EC: 4.1.3.2

-
Non-polymers , 6 types, 649 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE / Glyoxylic acid


Mass: 74.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulphate, MES pH 6.5, Dioxane, magnesium chloride, acetyl coenzyme A, glyoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
22 mMacetyl-CoA1drop
32 mMglyoxylate1drop
420 mMTris-HCl1droppH8.0
51.6 Mammonium sulfate1reservoir
60.1 MMES1reservoirpH6.5
710 %dioxane1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2000 / Details: mirrors
RadiationMonochromator: bend cylindrical Ge(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 51936 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / % possible all: 93.9
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. measured all: 397417 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.33

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.36 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.858 / SU B: 17.822 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28719 4591 10.1 %RANDOM
Rwork0.19049 ---
all0.2002 43284 --
obs0.2002 40817 94.3 %-
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: 25.996 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10960 0 97 639 11696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02111260
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.95815320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81451428
X-RAY DIFFRACTIONr_chiral_restr0.0870.21744
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028586
X-RAY DIFFRACTIONr_nbd_refined0.2140.25988
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2611
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.211
X-RAY DIFFRACTIONr_mcbond_it0.3911.57114
X-RAY DIFFRACTIONr_mcangle_it0.734211437
X-RAY DIFFRACTIONr_scbond_it0.93334146
X-RAY DIFFRACTIONr_scangle_it1.5944.53883
LS refinement shellResolution: 2.701→2.771 Å / Num. reflection Rfree: 308 / Num. reflection Rwork: 2772 / Total num. of bins used: 20
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.186

+
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