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- PDB-2c6x: Structure of Bacillus subtilis citrate synthase -

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Basic information

Entry
Database: PDB / ID: 2c6x
TitleStructure of Bacillus subtilis citrate synthase
ComponentsCITRATE SYNTHASE 1
KeywordsTRANSFERASE / TRICARBOXYLIC ACID CYCLE / CITRATE SYNTHASE / ALLOSTERIC ENZYME / BACILLUS SUBTILIS / ENZYME THERMOSTABILITY
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function
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, 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / COENZYME A / Citrate synthase 1
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsVogl, C. / Hough, D.W. / Danson, M.J. / Crennell, S.J.
CitationJournal: To be Published
Title: Domain Closure in Citrate Synthases Adapted to the Range of Biological Temperatures
Authors: Vogl, C. / Hough, D.W. / Danson, M.J. / Crennell, S.J.
History
DepositionNov 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CITRATE SYNTHASE 1
B: CITRATE SYNTHASE 1
C: CITRATE SYNTHASE 1
D: CITRATE SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,54312
Polymers162,7054
Non-polymers3,8398
Water0
1
A: CITRATE SYNTHASE 1
B: CITRATE SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2726
Polymers81,3522
Non-polymers1,9194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CITRATE SYNTHASE 1
D: CITRATE SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2726
Polymers81,3522
Non-polymers1,9194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.504, 185.563, 82.563
Angle α, β, γ (deg.)90.00, 106.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.14882, -0.96021, 0.23634), (-0.96339, -0.19469, -0.18434), (0.22301, -0.20026, -0.95402)-4.11307, 10.02055, 62.42325
2given(-0.99715, 0.05461, -0.05207), (-0.05308, -0.99813, -0.03027), (-0.05362, -0.02742, 0.99818)3.72114, 142.06503, -0.26935
3given(-0.19478, 0.9574, -0.21317), (0.94984, 0.23833, 0.20248), (0.24466, -0.16304, -0.9558)5.7763, 130.47935, 61.62028

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Components

#1: Protein
CITRATE SYNTHASE 1 / / CITRATE SYNTHASE I


Mass: 40676.176 Da / Num. of mol.: 4 / Fragment: RESIDUES, 2-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Variant: DSM 402 / Plasmid: PREC7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MOB154 / References: UniProt: P39119, citrate (Si)-synthase
#2: Chemical
ChemComp-COZ / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
Sequence detailsONE CHANGE INTRODUCED IN CLONING, RESIDUE 94 IS L INSTEAD OF V

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 8 / Details: 0.1M LI2SO4, 0.1M TRIS PH8.0, 30%PEG4K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 12, 2002 / Details: MSCOSMIC BLUE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→29.8 Å / Num. obs: 20446 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.72
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.17 / % possible all: 91.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A59

1a59


Resolution: 3.4→29.81 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1336326.15 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1048 5.1 %RANDOM
Rwork0.284 ---
obs0.284 20410 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.240453 e/Å3
Displacement parametersBiso mean: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1-10.47 Å20 Å2-0.65 Å2
2---11.85 Å20 Å2
3---1.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3.4→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11428 0 244 0 11672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.53
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
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 160 5 %
Rwork0.345 3059 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2COZ_NEWH.PARCOZ_NEWH.TOP
X-RAY DIFFRACTION3CIT_XPLOR.PARCIT_XPLOR.TOP

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