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- PDB-4jad: STRUCTURAL DETERMINATION OF THE A50T:S279G:S280K:V281K:K282E:H283... -

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Basic information

Entry
Database: PDB / ID: 4jad
TitleSTRUCTURAL DETERMINATION OF THE A50T:S279G:S280K:V281K:K282E:H283N VARIANT OF CITRATE SYNTHASE from E. COLI
ComponentsCitrate synthase
KeywordsTRANSFERASE / CITRATE SYNTHASE / GRAM-NEGATIVE BACTERIA / ALLOSTERY / OXALOACETATE / ACETYLCOA / NADH / ALLOSTERIC ENZYME / TRICARBOXYLIC ACID CYCLE
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / : / NADH binding / protein hexamerization / tricarboxylic acid cycle / identical protein binding / cytosol
Similarity search - Function
Rubrerythrin, domain 2 - #60 / Citrate synthase, type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain ...Rubrerythrin, domain 2 - #60 / Citrate synthase, type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Rubrerythrin, domain 2 / Single Sheet / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaurus, R. / Brayer, G.D.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Enzyme-substrate complexes of allosteric citrate synthase: Evidence for a novel intermediate in substrate binding.
Authors: Duckworth, H.W. / Nguyen, N.T. / Gao, Y. / Donald, L.J. / Maurus, R. / Ayed, A. / Bruneau, B. / Brayer, G.D.
History
DepositionFeb 18, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJul 17, 2013ID: 3L96
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Sep 20, 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 / 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 / _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: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3746
Polymers95,9902
Non-polymers3844
Water9,476526
1
A: Citrate synthase
B: Citrate synthase
hetero molecules

A: Citrate synthase
B: Citrate synthase
hetero molecules

A: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,12118
Polymers287,9696
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area45250 Å2
ΔGint-395 kcal/mol
Surface area95160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.513, 165.513, 159.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Citrate synthase


Mass: 47994.785 Da / Num. of mol.: 2 / Mutation: A50T, S279G, S280K, V281K, K282E, H283N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: gltA, gluT, icdB, b0720, JW0710 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABH7, citrate (Si)-synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsASPARTATE AT POSITION 10 CHAIN A AND 1010 CHAIN B IS A POST-TRANSLATIONAL MODIFICATION OF ASN THAT ...ASPARTATE AT POSITION 10 CHAIN A AND 1010 CHAIN B IS A POST-TRANSLATIONAL MODIFICATION OF ASN THAT IS CONSISTENTLY OBSERVED IN MASS SPECTROMETRY AND EDMAN DEGRADATION MEASUREMENTS.

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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: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG, 2.0-2.3 M AMMONIUM SULFATE, 0.1 M NA HEPES, PH 7.5, HANGING DROP, TEMPERATURE 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2008 / Details: VERTICAL FOCUSING MIRROR
RadiationMonochromator: SIDE SCATTERING I-BEAM BENT SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 124116 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.3

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Processing

Software
NameClassification
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K3P

1k3p
PDB Unreleased entry


Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.217 5921 4.6 %RANDOM
Rwork0.194 ---
obs0.194 121151 94.2 %-
Solvent computationBsol: 83.42 Å2
Displacement parametersBiso mean: 32.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6730 0 20 526 7276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION3SUL.PAR
X-RAY DIFFRACTION4ION.PAR

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