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- PDB-2jqx: Solution structure of Malate Synthase G from joint refinement aga... -

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Basic information

Entry
Database: PDB / ID: 2jqx
TitleSolution structure of Malate Synthase G from joint refinement against NMR and SAXS data
ComponentsMalate synthase G
KeywordsTRANSFERASE / APO-MALATE SYNTHASE G / 82 KDA ENZYME / SAXS / SMALL-ANGLE X-RAY SCATTERING / RDC / RESIDUAL DIPOLAR COUPLING / residual chemical shift anisotropy / ALIGNMENT / deuteration
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
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, Cartesian molecular dynamics
AuthorsGrishaev, A. / Tugarinov, V. / Kay, L.E. / Trewhella, J. / Bax, A.
Citation
Journal: J.Biomol.Nmr / Year: 2008
Title: Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints
Authors: Grishaev, A. / Tugarinov, V. / Kay, L.E. / Trewhella, J. / Bax, A.
#2: Journal: PROC.NATL.ACAD.SCI.USA / Year: 2005
Title: Solution NMR-derived global fold of a monomeric 82-kDa enzyme
Authors: Tugarinov, V. / Choy, W. / Orekhov, V.Y. / Kay, L.E.
#3: Journal: J.AM.CHEM.SOC. / Year: 2005
Title: Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data
Authors: Grishaev, A. / Wu, J. / Trewhella, J. / Bax, A.
History
DepositionJun 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Remark 950THIS ENTRY 2JQX REFLECTS A JOINT MODELING OF THE STRUCTURAL DATA IN RCSB031242.MR PDB ENTRY 1Y8B ...THIS ENTRY 2JQX REFLECTS A JOINT MODELING OF THE STRUCTURAL DATA IN RCSB031242.MR PDB ENTRY 1Y8B AND ADDITIONAL SAX DATA. INFORMATION IN REMARK 210 SERIES IS BASED ON SAX AND THE EXPERIMENT DESCRIBED IN PDB ENTRY 1Y8B. ORIGINAL DATA DETERMINED BY AUTHOR: V.TUGARINOV, W.-Y.CHOY, V.Y.OREKHOV, L.E.KAY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate synthase G


Theoretical massNumber of molelcules
Total (without water)80,5651
Polymers80,5651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 5closest to the average
RepresentativeModel #1closest to the average

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Components

#1: Protein Malate synthase G / MSG


Mass: 80565.344 Da / Num. of mol.: 1 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glcB, glc / Production host: Escherichia coli (E. coli) / References: UniProt: P37330, malate synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D TROSY-based NOESY
1214D TROSY-based NOESY
1313D TROSY-HNCO
NMR detailsText: Experimental small-angle X-ray scattering data were acquired at the beam line 4-2, SSRL, using incident radiation at the 8 keV and 1.25 m sample-to-detector distance. One-dimensional gas ...Text: Experimental small-angle X-ray scattering data were acquired at the beam line 4-2, SSRL, using incident radiation at the 8 keV and 1.25 m sample-to-detector distance. One-dimensional gas position-sensitive detector was used for data collection. EXPERIMENTAL NMR DATA used for structure refinement are THE SAME AS IN THE PDB DEPOSITION 1Y8B (citation 1). SAXS intensities OVER THE RANGE Q = 0.028 TO 0.780 A-1 were FITTED BY A supplementary MODULE as described in citation 2.

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Sample preparation

DetailsContents: 0.17 mM [U-100% 15N], Ile CD1-[13CH3] MALATE SYNTHASE G, 20 mM sodium phosphate, 5 mM DTT, 150 mM sodium chloride, 100% H2O
Solvent system: 100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.17 mMMALATE SYNTHASE G[U-100% 15N], Ile CD1-[13CH3]1
20 mMsodium phosphate1
5 mMDTT1
150 mMsodium chloride1
Sample conditionsIonic strength: 170 / pH: 7.1 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
OTOKOKochdata reduction
PRIMUSSvergundata processing
RefinementMethod: simulated annealing, Cartesian molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: closest to the average / Conformers calculated total number: 5 / Conformers submitted total number: 1

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