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- PDB-1n8i: Biochemical and Structural Studies of Malate Synthase from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 1n8i
TitleBiochemical and Structural Studies of Malate Synthase from Mycobacterium tuberculosis
ComponentsProbable malate synthase G
KeywordsLYASE / malate synthase / glyoxylate pathway / Mycobacterium tuberculosis / acetyl coenzyme A / isocitrate lyase / persistence / GLCB / 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 cycle / glyoxylate catabolic process / 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 cycle / glyoxylate catabolic process / fibronectin binding / laminin binding / tricarboxylic acid cycle / peptidoglycan-based cell wall / manganese ion binding / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm / cytosol
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
GLYOXYLIC ACID / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5873
Polymers80,4891
Non-polymers982
Water8,107450
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.095, 78.095, 223.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHE BIOLOGICAL ASSEMBLY IS A MONOMER

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Components

#1: Protein Probable malate synthase G


Mass: 80488.797 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


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


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 292 K / Method: microbatch / pH: 8.5
Details: PEG 4000, MAGNESIUM CHLORIDE,Tris-HCl pH 8.5, MICROBATCH, temperature 292K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13-5 mg/mlprotein11
215 %(w/v)PEG400011
30.05 MTris-HCl11pH8.5
40.05 M11MgCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.033
SYNCHROTRONAPS 19-ID20.9794, 0.9792, 0.9421, 1.0197
Detector
TypeIDDetectorDateDetails
CUSTOM-MADE1CCDJun 20, 1999mirrors
CUSTOM-MADE2CCDJun 20, 1999mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromator Si-111 and double crystal monochromator Si-220SINGLE WAVELENGTHMx-ray1
2double crystal monochromator Si-111 and double crystal monochromator Si-220MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
20.97941
30.97921
40.94211
51.01971
ReflectionResolution: 2.1→30 Å / Num. obs: 39261 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 85.7
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 95.2 % / Num. measured all: 141203 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 85.7 % / Rmerge(I) obs: 0.28

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2306 3636 Random
Rwork0.1853 --
all0.1921 39261 -
obs0.1853 36311 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 6 450 5824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004888
X-RAY DIFFRACTIONc_angle_deg1.26531
X-RAY DIFFRACTIONc_dihedral_angle_d21.55191
X-RAY DIFFRACTIONc_improper_angle_d0.76241
LS refinement shellResolution: 2.1→2.18 Å /
RfactorNum. reflection
Rfree0.2336 321
Rwork0.1784 -
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0049
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.55191
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76241

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