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- PDB-8xu1: DaCS-oxaloacetate complex -

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Basic information

Entry
Database: PDB / ID: 8xu1
TitleDaCS-oxaloacetate complex
Componentscitrate synthase
KeywordsTRANSFERASE / citrate synthase / citrate cleavage / reversible
Function / homology
Function and homology information


citrate synthase activity / 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
OXALOACETATE ION / citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesDesulfurella acetivorans A63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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: DaCS-oxaloacetate complex
Authors: Yang, L. / Fang, Y.J.
History
DepositionJan 12, 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)147,1756
Polymers146,7823
Non-polymers3933
Water2,144119
1
A: citrate synthase
B: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1174
Polymers97,8552
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-65 kcal/mol
Surface area30070 Å2
MethodPISA
2
C: citrate synthase
hetero molecules

C: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1174
Polymers97,8552
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10280 Å2
ΔGint-64 kcal/mol
Surface area29840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.100, 111.280, 99.560
Angle α, β, γ (deg.)90.00, 116.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein citrate synthase


Mass: 48927.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfurella acetivorans A63 (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A7C6A739, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 53.21 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M KCl, 0.05 M HEPES pH 7.5, 35% v/v Pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.46→45.11 Å / Num. obs: 54679 / % possible obs: 98.98 % / Redundancy: 3.3 % / CC1/2: 0.981 / Rmerge(I) obs: 0.182 / Rrim(I) all: 0.255 / Net I/σ(I): 6.7
Reflection shellResolution: 2.46→2.52 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.366 / Num. unique obs: 3830 / CC1/2: 0.311 / Rpim(I) all: 0.985 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→45.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 14.4 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 0.533 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25756 2662 4.9 %RANDOM
Rwork0.21109 ---
obs0.21335 51987 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.05 Å2
2---0.24 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 2.46→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10275 0 27 122 10424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01210563
X-RAY DIFFRACTIONr_bond_other_d0.0020.0169786
X-RAY DIFFRACTIONr_angle_refined_deg1.471.64414313
X-RAY DIFFRACTIONr_angle_other_deg0.4591.55722812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97651299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.4629.73757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.772101809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21548
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022073
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_it5.2145.8565205
X-RAY DIFFRACTIONr_mcbond_other5.2125.8565205
X-RAY DIFFRACTIONr_mcangle_it7.7298.7686501
X-RAY DIFFRACTIONr_mcangle_other7.7298.7696502
X-RAY DIFFRACTIONr_scbond_it5.786.3795358
X-RAY DIFFRACTIONr_scbond_other5.7796.3795358
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9469.3577813
X-RAY DIFFRACTIONr_long_range_B_refined11.47773.20612037
X-RAY DIFFRACTIONr_long_range_B_other11.47773.21312036
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 215 -
Rwork0.376 3830 -
obs--99.05 %

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