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- PDB-3saz: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

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Basic information

Entry
Database: PDB / ID: 3saz
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 4-(3-bromophenyl)-2,4-dioxobutanoic acid inhibitor
ComponentsMalate synthase G
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitor complex / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / malate synthase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / glyoxylate catabolic process / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding ...host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / glyoxylate catabolic process / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic 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 / cytoplasm / cytosol
Similarity search - Function
Malate synthase G - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / Malate synthase G / : / Malate synthase G, alpha-beta insertion domain / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase / Malate synthase superfamily ...Malate synthase G - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / Malate synthase G / : / Malate synthase G, alpha-beta insertion domain / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase / Malate synthase superfamily / Malate synthase, C-terminal superfamily / Malate synthase, N-terminal and TIM-barrel domains / : / : / Malate synthase, TIM barrel domain / Malate synthase, N-terminal domain / Malate synthase, C-terminal / Beta Complex / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-(3-bromophenyl)-2,4-dioxobutanoic acid / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.04 Å
AuthorsKrieger, I.V. / Sun, Q. / Sacchettini, J.C. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: Chem.Biol. / Year: 2012
Title: Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase.
Authors: Krieger, I.V. / Freundlich, J.S. / Gawandi, V.B. / Roberts, J.P. / Gawandi, V.B. / Sun, Q. / Owen, J.L. / Fraile, M.T. / Huss, S.I. / Lavandera, J.L. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Other
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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.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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8015
Polymers80,4571
Non-polymers3444
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.216, 78.216, 223.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Malate synthase G


Mass: 80456.734 Da / Num. of mol.: 1 / Mutation: c619A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glcB, GlcB (Rv1837c), MT1885, MTCY1A11.06, Rv1837c / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5J4, UniProt: P9WK17*PLUS, malate synthase
#2: Chemical ChemComp-043 / 4-(3-bromophenyl)-2,4-dioxobutanoic acid


Mass: 271.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7BrO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDEVIATIONS FROM SP2 GEOMETRY POTENTIALLY ARE DUE TO CHARGE INFLUENCING INTERACTIONS WITH THE PROTEIN.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 0.1 M magnesium chloride, 0.1 M TRIS-HCl , VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 8.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å
DetectorType: 2 x 2 mosaic CCD detector / Detector: CCD / Date: Feb 9, 2008
RadiationMonochromator: double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.89→49.57 Å / Num. all: 56204 / Num. obs: 56104 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.3 % / Rmerge(I) obs: 0.099 / Rsym value: 0.066 / Net I/σ(I): 6.3
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.785 / % possible all: 40.5

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
REFMACrefinement
PHENIXmodel building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
PHENIXphasing
HKL-2000data collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1N8I

1n8i


Resolution: 2.04→49.57 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.9497 / SU ML: 0.22 / σ(F): 1.89 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 2251 5 %
Rwork0.1628 --
obs0.1649 45023 99.53 %
all-56204 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.899 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3089 Å20 Å2-0 Å2
2--3.3089 Å2-0 Å2
3----6.6178 Å2
Refine analyzeLuzzati coordinate error obs: 0.192 Å
Refinement stepCycle: LAST / Resolution: 2.04→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5456 0 18 574 6048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075635
X-RAY DIFFRACTIONf_angle_d1.0137671
X-RAY DIFFRACTIONf_dihedral_angle_d13.9432084
X-RAY DIFFRACTIONf_chiral_restr0.066877
X-RAY DIFFRACTIONf_plane_restr0.0071009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.08440.25881290.19422605X-RAY DIFFRACTION99
2.0844-2.13290.22161400.18162606X-RAY DIFFRACTION99
2.1329-2.18620.25361410.17662589X-RAY DIFFRACTION99
2.1862-2.24530.22391300.16472614X-RAY DIFFRACTION99
2.2453-2.31140.20721440.16582617X-RAY DIFFRACTION99
2.3114-2.3860.25521150.16832658X-RAY DIFFRACTION100
2.386-2.47130.24211460.16532613X-RAY DIFFRACTION99
2.4713-2.57020.20431290.16242664X-RAY DIFFRACTION100
2.5702-2.68720.20731430.16732669X-RAY DIFFRACTION100
2.6872-2.82880.21981470.17582636X-RAY DIFFRACTION100
2.8288-3.0060.22571360.17922691X-RAY DIFFRACTION100
3.006-3.23810.25651560.17952674X-RAY DIFFRACTION100
3.2381-3.56390.18151560.15812694X-RAY DIFFRACTION100
3.5639-4.07940.17371440.14392723X-RAY DIFFRACTION100
4.0794-5.13870.17771440.13632776X-RAY DIFFRACTION100
5.1387-49.58650.17761510.17212943X-RAY DIFFRACTION100

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