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- PDB-8xxe: TtCS-intermediate complex -

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Basic information

Entry
Database: PDB / ID: 8xxe
TitleTtCS-intermediate complex
ComponentsCitrate synthase
KeywordsTRANSFERASE / citrate synthase / citrate cleavage / reversible
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 GROUP / COENZYME A / OXALOACETATE ION / Citrate synthase
Similarity search - Component
Biological speciesThermosulfidibacter takaii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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-intermediate 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,04210
Polymers153,3023
Non-polymers2,7407
Water10,773598
1
A: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9996
Polymers102,2012
Non-polymers1,7974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-56 kcal/mol
Surface area30980 Å2
MethodPISA
2
C: Citrate synthase
hetero molecules

C: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0878
Polymers102,2012
Non-polymers1,8856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12680 Å2
ΔGint-57 kcal/mol
Surface area30060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.910, 109.910, 265.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-773-

HOH

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Components

#1: Protein Citrate synthase / CS


Mass: 51100.664 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-TRIS pH 6.5, 2.4M 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: Jan 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.08→34.46 Å / Num. obs: 98252 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rrim(I) all: 0.189 / Net I/σ(I): 19.3
Reflection shellResolution: 2.08→2.13 Å / Rmerge(I) obs: 1.313 / Num. unique obs: 7160 / CC1/2: 0.896 / Rpim(I) all: 0.363

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→34.46 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.889 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21672 4900 5 %RANDOM
Rwork0.17098 ---
obs0.17326 93238 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.132 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.08→34.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10694 0 174 598 11466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01211180
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610442
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.65815177
X-RAY DIFFRACTIONr_angle_other_deg0.481.5724041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31251340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.435590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.966101843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.21611
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022606
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_it3.4473.7955365
X-RAY DIFFRACTIONr_mcbond_other3.4473.7965366
X-RAY DIFFRACTIONr_mcangle_it4.4486.8046702
X-RAY DIFFRACTIONr_mcangle_other4.4486.8046703
X-RAY DIFFRACTIONr_scbond_it4.7664.3935815
X-RAY DIFFRACTIONr_scbond_other4.7664.3945816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0187.8498476
X-RAY DIFFRACTIONr_long_range_B_refined8.05738.413281
X-RAY DIFFRACTIONr_long_range_B_other8.05838.213172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 335 -
Rwork0.204 6791 -
obs--100 %

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