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- PDB-2gq3: mycobacterium tuberculosis malate synthase in complex with magnes... -

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Basic information

Entry
Database: PDB / ID: 2gq3
Titlemycobacterium tuberculosis malate synthase in complex with magnesium, malate, and coenzyme A
ComponentsMalate synthase G
KeywordsTRANSFERASE / TIM barrel / coenzyme A
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
COENZYME A / D-MALATE / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAnstrom, D.M. / Remington, S.J.
CitationJournal: Protein Sci. / Year: 2006
Title: The product complex of M. tuberculosis malate synthase revisited.
Authors: Anstrom, D.M. / Remington, S.J.
History
DepositionApr 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
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 / 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.ptnr1_label_seq_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.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_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

Downloads & links

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Assembly

Deposited unit
A: Malate synthase G
B: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,05211
Polymers158,4432
Non-polymers1,6109
Water11,115617
1
A: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4106
Polymers79,2211
Non-polymers1,1895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6425
Polymers79,2211
Non-polymers4214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.380, 120.380, 238.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Malate synthase G


Mass: 79221.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glcB / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3)
References: UniProt: P0A5J4, UniProt: P9WK17*PLUS, malate synthase

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Non-polymers , 5 types, 626 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 23% PEG-8000, 14% MPD, 0.2 M magnesium acetate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.95371
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2004
RadiationMonochromator: KOHZU: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 78420 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.9 / % possible all: 98.6

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Phasing

Phasing MRRfactor: 0.46 / Cor.coef. Fo:Fc: 0.46
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N8I

1n8i


Resolution: 2.3→49.09 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 8.663 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / σ(F): 0 / ESU R: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.244 7746 -RANDOM
Rwork0.178 ---
obs0.174 78155 99.4 %-
all-78626 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10916 0 100 617 11633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02211219
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.96415270
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60251428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84724.112501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.366151781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2331585
X-RAY DIFFRACTIONr_chiral_restr0.1310.21741
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028541
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.25623
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.27667
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2762
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0351.57321
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.594211430
X-RAY DIFFRACTIONr_scbond_it2.89934409
X-RAY DIFFRACTIONr_scangle_it4.2184.53840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.228 5654 -
obs--98.6 %
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)
11.6894-0.0604-0.2571.05530.15020.81440.0649-0.0174-0.01050.09110.0288-0.02970.003-0.0062-0.0938-0.2297-0.0061-0.0165-0.1920.0212-0.191255.352234.835987.409
22.4460.03620.44341.73941.04853.3354-0.09840.5862-0.3896-0.14720.18870.03090.18510.08-0.0903-0.0985-0.0318-0.02440.125-0.1034-0.094649.157316.752555.3938
31.4151-0.1911-0.86762.36260.38792.58110.00290.01090.0115-0.46040.0052-0.3964-0.63950.1059-0.00810.2384-0.06610.1169-0.14060.0111-0.032762.3399-27.069974.8203
44.1101-1.23021.08454.06270.23135.78230.33880.36280.1007-0.7954-0.24090.8842-0.8582-1.0642-0.09790.50650.3262-0.04760.24380.03980.220529.531-9.644179.3229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1344 - 136
2X-RAY DIFFRACTION1AA265 - 315267 - 317
3X-RAY DIFFRACTION1AA333 - 727335 - 729
4X-RAY DIFFRACTION2AA135 - 264137 - 266
5X-RAY DIFFRACTION2AA316 - 332318 - 334
6X-RAY DIFFRACTION3BB2 - 1344 - 136
7X-RAY DIFFRACTION3BB265 - 315267 - 317
8X-RAY DIFFRACTION3BB333 - 726335 - 728
9X-RAY DIFFRACTION4BB135 - 264137 - 266
10X-RAY DIFFRACTION4BB316 - 332318 - 334

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