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- PDB-2r9e: The structure of the binary complex of citryl dethia COA and citr... -

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Basic information

Entry
Database: PDB / ID: 2r9e
TitleThe structure of the binary complex of citryl dethia COA and citrate synthase from the thermophilic archaeonthermoplasma acidophilum
ComponentsCitrate synthase
KeywordsTRANSFERASE / CITRATE SYNTHASE / Citryl Dethia Cenzyme A / EC 2.3.3.1 / Allosteric enzyme / Tricarboxylic acid cycle
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate synthase activity / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
2-methylcitrate synthase/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 ...2-methylcitrate synthase/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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
s-citryldethia Coenzyme A / Citrate synthase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLehmann, C. / Chen, Z.
CitationJournal: To be Published
Title: Snapshots of Intermediates in the Condensation Reaction Catalyzed by Citrate Synthase
Authors: Lehmann, C. / Kurz, L.C. / Ellenberger, T.E.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
C: Citrate synthase
D: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,2128
Polymers172,5094
Non-polymers3,7024
Water24,7351373
1
A: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1064
Polymers86,2552
Non-polymers1,8512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-38 kcal/mol
Surface area26970 Å2
MethodPISA
2
C: Citrate synthase
D: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1064
Polymers86,2552
Non-polymers1,8512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-33 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.061, 73.498, 89.983
Angle α, β, γ (deg.)99.35, 98.19, 113.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Citrate synthase /


Mass: 43127.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermoplasma acidophilum (acidophilic) / References: UniProt: P21553, citrate (Si)-synthase
#2: Chemical
ChemComp-SDX / s-citryldethia Coenzyme A


Mass: 925.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H46N7O22P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1373 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17 % PEG 4000, 100MM HEPES, 200MM SODIUM ACETATE, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 106109 / % possible obs: 97.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.118 / Rsym value: 0.124 / Net I/σ(I): 27.5
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.317 / % possible all: 79.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→33.28 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.673 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21485 5292 5 %RANDOM
Rwork0.15692 ---
obs0.15984 100554 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.176 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20.02 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11972 0 240 1373 13585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212477
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.98216908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62351522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26123.875542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.298152147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8291576
X-RAY DIFFRACTIONr_chiral_restr0.1190.21843
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219324
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.26512
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.28751
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2992
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.57558
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.668212157
X-RAY DIFFRACTIONr_scbond_it2.78234919
X-RAY DIFFRACTIONr_scangle_it4.5784.54747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 290 -
Rwork0.207 5702 -
obs--74.61 %

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