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- PDB-8xxf: TtCS, oxaloacetate, acetyl-CoA complex -

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Basic information

Entry
Database: PDB / ID: 8xxf
TitleTtCS, oxaloacetate, acetyl-CoA complex
ComponentsCitrate synthase
KeywordsTRANSFERASE / citrate synthase / citrate cleavage / reversible / high-temperature crystal
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / : / tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function
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
Similarity search - Domain/homology
ACETYL COENZYME *A / COENZYME A / OXALOACETATE ION / Citrate synthase
Similarity search - Component
Biological speciesThermosulfidibacter takaii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsYang, L. / Fang, Y.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: TtCS, oxaloacetate, acetyl-CoA complex
Authors: Yang, L. / Fang, Y.J.
History
DepositionJan 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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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
E: Citrate synthase
F: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,64614
Polymers306,6046
Non-polymers3,0428
Water15,907883
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.490, 131.760, 207.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Citrate synthase / CS


Mass: 51100.664 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosulfidibacter takaii (bacteria) / Gene: gltA, TST_0783 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0S3QTD0, citrate synthase (unknown stereospecificity)
#2: Chemical
ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 883 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 333.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 6.5, 2.4 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.33→30.15 Å / Num. obs: 127185 / % possible obs: 99.9 % / Redundancy: 11.7 % / CC1/2: 0.983 / Rmerge(I) obs: 0.319 / Rpim(I) all: 0.139 / Rrim(I) all: 0.349 / Net I/σ(I): 5.9
Reflection shellResolution: 2.33→2.39 Å / Rmerge(I) obs: 2.213 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 9287 / CC1/2: 0.449

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→30.15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.427 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 6296 5 %RANDOM
Rwork0.18654 ---
obs0.18941 120779 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å20 Å2
2---0.18 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.33→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21435 0 0 883 22318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01222024
X-RAY DIFFRACTIONr_bond_other_d0.0010.01620642
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.8529871
X-RAY DIFFRACTIONr_angle_other_deg0.5651.75547538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72852643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.4345174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.641103685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.23168
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0225919
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025136
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2843.74410590
X-RAY DIFFRACTIONr_mcbond_other3.2873.74410590
X-RAY DIFFRACTIONr_mcangle_it4.9926.72113222
X-RAY DIFFRACTIONr_mcangle_other4.9936.72213223
X-RAY DIFFRACTIONr_scbond_it4.0544.15811434
X-RAY DIFFRACTIONr_scbond_other4.0544.15911435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3317.46616649
X-RAY DIFFRACTIONr_long_range_B_refined8.61935.925740
X-RAY DIFFRACTIONr_long_range_B_other8.62935.9125644
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 482 -
Rwork0.395 8737 -
obs--99.73 %

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