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- PDB-8xu2: DaCS-citrate complex -

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Basic information

Entry
Database: PDB / ID: 8xu2
TitleDaCS-citrate 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
CITRIC ACID / citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesDesulfurella acetivorans A63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsYang, L.Y. / Fang, Y.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: DaCS-citrate complex
Authors: Yang, L.Y. / 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
D: citrate synthase
E: citrate synthase
F: citrate synthase
G: citrate synthase
H: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,12616
Polymers393,5898
Non-polymers1,5378
Water27,4011521
1
A: citrate synthase
B: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7814
Polymers98,3972
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-64 kcal/mol
Surface area29750 Å2
MethodPISA
2
C: citrate synthase
D: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7814
Polymers98,3972
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-63 kcal/mol
Surface area29570 Å2
MethodPISA
3
E: citrate synthase
F: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7814
Polymers98,3972
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-63 kcal/mol
Surface area29620 Å2
MethodPISA
4
G: citrate synthase
H: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7814
Polymers98,3972
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-63 kcal/mol
Surface area29600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)362.335, 362.335, 77.886
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
citrate synthase


Mass: 49198.590 Da / Num. of mol.: 8
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1521 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium chloride, 0.1 M HEPES pH 7.5 and 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: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.18→24.66 Å / Num. obs: 191541 / % possible obs: 97.5 % / Redundancy: 8.2 % / CC1/2: 0.991 / Net I/σ(I): 32
Reflection shellResolution: 2.19→2.22 Å / Redundancy: 8 % / Rmerge(I) obs: 0.567 / Num. unique obs: 9494 / CC star: 0.964 / Rpim(I) all: 0.21 / Rrim(I) all: 0.606

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→24.66 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.398 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20347 9668 5.1 %RANDOM
Rwork0.17488 ---
obs0.17633 181722 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.19→24.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27443 0 104 1522 29069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01228299
X-RAY DIFFRACTIONr_bond_other_d0.0010.01626163
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.64338377
X-RAY DIFFRACTIONr_angle_other_deg0.4341.55660995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42553491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.98510144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.741104828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.24155
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0231853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025547
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_it3.2583.85913940
X-RAY DIFFRACTIONr_mcbond_other3.2583.85913940
X-RAY DIFFRACTIONr_mcangle_it4.7475.77417415
X-RAY DIFFRACTIONr_mcangle_other4.7475.77517416
X-RAY DIFFRACTIONr_scbond_it3.5054.12314359
X-RAY DIFFRACTIONr_scbond_other3.5044.12414356
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2796.0720955
X-RAY DIFFRACTIONr_long_range_B_refined7.13248.20933881
X-RAY DIFFRACTIONr_long_range_B_other7.12448.00733607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 731 -
Rwork0.236 13244 -
obs--96.64 %

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