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- PDB-1d8c: MALATE SYNTHASE G COMPLEXED WITH MAGNESIUM AND GLYOXYLATE -

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Basic information

Entry
Database: PDB / ID: 1d8c
TitleMALATE SYNTHASE G COMPLEXED WITH MAGNESIUM AND GLYOXYLATE
ComponentsMALATE SYNTHASE G
KeywordsLYASE / ALPHA-BETA BARREL / TIM BARREL / GLYOXYLATE CYCLE / ENOLIZATION / CONDENSATION / CONCERTED ACID-BASE CATALYSIS
Function / homology
Function and homology information


malate synthase / malate synthase activity / glyoxylate cycle / glyoxylate catabolic process / 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, 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 / sorbitol / Malate synthase G
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsHoward, B.R. / Endrizzi, J.A. / Remington, S.J.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 A resolution: mechanistic implications.
Authors: Howard, B.R. / Endrizzi, J.A. / Remington, S.J.
History
DepositionOct 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALATE SYNTHASE G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4059
Polymers81,6441
Non-polymers7618
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.800, 88.700, 109.900
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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Protein / Sugars , 2 types, 2 molecules A

#1: Protein MALATE SYNTHASE G


Mass: 81643.945 Da / Num. of mol.: 1 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Details: C-terminal his-tag (724-731) / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET-28B / Production host: Escherichia coli (E. coli) / References: UniProt: P37330, EC: 4.1.3.2
#2: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O6

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Non-polymers , 4 types, 352 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


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


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.2 Å3/Da / Density % sol: 44 %
Description: selenium positions located with shake-n-bake v.2. Number of unique reflections and overall data redundancy includes separated friedel pairs.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, sorbitol, imidazole, magnesium, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.8 Mammonium sulfate1reservoir
2100 mMimidazole1reservoirpH8.0
350 mMsorbitol1reservoir
424 mg/mlenzyme1drop
514 mM1dropMgCl2
67 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.008
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 94144 / Num. obs: 93570 / % possible obs: 99.4 % / Redundancy: 3.93 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.7 / Num. unique all: 9222 / % possible all: 98
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 367712
Reflection shell
*PLUS
% possible obs: 98 % / Mean I/σ(I) obs: 2.7

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Processing

Software
NameClassification
SHARPphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Isotropic thermal model: TNT CORRELATED B'S / Stereochemistry target values: TNT GEOMETRY LIBRARY
Details: This model has been refined against the combined working and test set.
Num. reflection% reflectionSelection details
all49429 --
obs49242 99.6 %-
Rfree--RANDOM, USING HKL SEGREGATE OPTION IN TNT
Solvent computationSolvent model: TNT / Bsol: 261.252 Å2 / ksol: 0.83594 e/Å3
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5331 0 43 345 5719
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01554720.7
X-RAY DIFFRACTIONt_angle_deg2.48674251.2
X-RAY DIFFRACTIONt_dihedral_angle_d15.9632360
X-RAY DIFFRACTIONt_trig_c_planes0.0181450.7
X-RAY DIFFRACTIONt_gen_planes0.0168033.4
X-RAY DIFFRACTIONt_it4.5953881
X-RAY DIFFRACTIONt_nbd0.0286110
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection all: 49242 / Num. reflection Rfree: 2522 / % reflection Rfree: 5 % / Rfactor all: 0.177 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d0.7
X-RAY DIFFRACTIONt_angle_deg1.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg015.96
X-RAY DIFFRACTIONt_planar_d0.70.018
X-RAY DIFFRACTIONt_plane_restr3.40.016

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