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- PDB-1p7t: Structure of Escherichia coli malate synthase G:pyruvate:acetyl-C... -

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Basic information

Entry
Database: PDB / ID: 1p7t
TitleStructure of Escherichia coli malate synthase G:pyruvate:acetyl-Coenzyme A abortive ternary complex at 1.95 angstrom resolution
Components(Malate synthase ...) x 2
KeywordsLYASE / TIM barrel / Glyoxylate cycle / Acetyl-COA / cysteine-sulfenic acid
Function / homology
Function and homology information


malate synthase / malate synthase activity / glyoxylate catabolic process / glyoxylate cycle / tricarboxylic acid cycle / magnesium ion binding / 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
ACETYL COENZYME *A / DI(HYDROXYETHYL)ETHER / PYRUVIC ACID / Malate synthase G
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAnstrom, D.M. / Kallio, K. / Remington, S.J.
CitationJournal: Protein Sci. / Year: 2003
Title: Structure of the Escherichia Coli Malate Synthase G:pyruvate:acetyl-coenzyme A Abortive Ternary Complex at 1.95 Angstrom Resolution
Authors: Anstrom, D.M. / Kallio, K. / Remington, S.J.
History
DepositionMay 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999Initiating Methionine

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)165,65911
Polymers163,3212
Non-polymers2,3389
Water10,503583
1
A: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6815
Polymers81,6531
Non-polymers1,0284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9796
Polymers81,6691
Non-polymers1,3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.931, 107.394, 204.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Malate synthase ... , 2 types, 2 molecules AB

#1: Protein Malate synthase G / MSG


Mass: 81652.516 Da / Num. of mol.: 1 / Mutation: S2A, C-terminal LEHHHHHH tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: GLCB OR GLC OR B2976 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109(DE3) / References: UniProt: P37330, malate synthase
#2: Protein Malate synthase G / MSG


Mass: 81668.516 Da / Num. of mol.: 1 / Mutation: S2A, C-terminal LEHHHHHH tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: GLCB OR GLC OR B2976 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109(DE3) / References: UniProt: P37330, malate synthase

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Non-polymers , 6 types, 592 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.9
Details: MgCl2, Tris, DTT, pyruvate, acetyl-Coenzyme A, HEPES, PEG-8000, sodium acetate, pH 7.9, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
127.7 mg/mlprotein1drop
28.3 mM1dropMgCl2
38.3 mMTris1droppH7.9
44.2 mMdithiothreitol1drop
550 mMpyruvate1drop
64.2 mMacetyl-CoA1drop
750 mMHEPES1reservoirpH7.0
8150 mMsodium acetate1reservoir
95 mM1reservoirMgCl2
1016 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.008 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.95→39.22 Å / Num. all: 108075 / Num. obs: 107535 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.06 Å / % possible all: 90.3
Reflection
*PLUS
Num. obs: 108075 / Redundancy: 3.3 % / Num. measured all: 591192 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 90.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
TNTrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D8C

1d8c


Resolution: 1.95→39.22 Å / Isotropic thermal model: TNT correlated B'S / σ(F): 0 / Stereochemistry target values: TNT Geometry Library
RfactorNum. reflectionSelection details
Rfree0.294 8437 random
Rwork0.194 --
all0.197 108075 -
obs0.197 107535 -
Refinement stepCycle: LAST / Resolution: 1.95→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10772 0 149 583 11504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg3
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_dihedral_angle_d1.5
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.022
X-RAY DIFFRACTIONt_angle_deg2.7
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg1.5

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