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- PDB-8xxc: DaCS-intermediate complex -

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Basic information

Entry
Database: PDB / ID: 8xxc
TitleDaCS-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
ACETIC ACID / CITRIC ACID / OXALOACETATE ION / citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesDesulfurella acetivorans A63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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-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
D: Citrate synthase
E: Citrate synthase
F: Citrate synthase
G: Citrate synthase
H: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,82418
Polymers391,2898
Non-polymers1,53510
Water36,4982026
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)361.422, 361.422, 77.741
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: 48911.148 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfurella acetivorans A63 (bacteria)
Strain: A63 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1G6J5C0, citrate synthase (unknown stereospecificity)
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2026 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH7.5, 40% v/v Polyethylene glycol 400

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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: 2.029→50 Å / Num. obs: 242593 / % possible obs: 99.1 % / Redundancy: 7.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.072 / Rrim(I) all: 0.199 / Net I/σ(I): 14.5
Reflection shellResolution: 2.029→2.07 Å / Rmerge(I) obs: 0.983 / Num. unique obs: 12183 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→25.07 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.566 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 11849 5 %RANDOM
Rwork0.196 ---
obs0.198 223879 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.03→25.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27401 0 104 2026 29531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01228170
X-RAY DIFFRACTIONr_bond_other_d0.0010.01626635
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.65338182
X-RAY DIFFRACTIONr_angle_other_deg0.481.57261572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8853463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.8175154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.907104787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.24124
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0232337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026151
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_it2.7753.39513881
X-RAY DIFFRACTIONr_mcbond_other2.7753.39513881
X-RAY DIFFRACTIONr_mcangle_it4.1566.09417333
X-RAY DIFFRACTIONr_mcangle_other4.1566.09517334
X-RAY DIFFRACTIONr_scbond_it2.8523.65914289
X-RAY DIFFRACTIONr_scbond_other2.8523.65914286
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4536.61720850
X-RAY DIFFRACTIONr_long_range_B_refined9.89232.6335351
X-RAY DIFFRACTIONr_long_range_B_other9.72432.5234931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 696 -
Rwork0.295 13761 -
obs--80.24 %

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