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- PDB-7wbr: Citrate synthase/lyase from Desulfurella acetivorans Desace_08345 -

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Basic information

Entry
Database: PDB / ID: 7wbr
TitleCitrate synthase/lyase from Desulfurella acetivorans Desace_08345
ComponentsCitrate synthase
KeywordsTRANSFERASE / Citrate synthase / probable citrate lyase / TCA / roTCA
Function / homology
Function and homology information


acyltransferase activity, acyl groups converted into alkyl on transfer / citrate synthase (unknown stereospecificity) / tricarboxylic acid cycle
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsYang, L.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Structure of Citrate synthase/lyase from Desulfurella acetivorans Desace_08345 complex with citrate
Authors: Yang, L.
History
DepositionDec 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)393,98816
Polymers392,4518
Non-polymers1,5378
Water17,529973
1
A: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4974
Polymers98,1132
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-69 kcal/mol
Surface area29220 Å2
MethodPISA
2
C: Citrate synthase
D: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4974
Polymers98,1132
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-68 kcal/mol
Surface area29220 Å2
MethodPISA
3
E: Citrate synthase
F: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4974
Polymers98,1132
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-71 kcal/mol
Surface area29290 Å2
MethodPISA
4
G: Citrate synthase
H: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4974
Polymers98,1132
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-68 kcal/mol
Surface area29240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)362.335, 362.335, 77.886
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Citrate synthase / / lyase Desace_08345


Mass: 49056.430 Da / Num. of mol.: 8 / Mutation: L3F/C48S/I99V/V207L/T278V/A309S/M330V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfurella acetivorans (bacteria) / Gene: ENO40_01140 / Production host: Escherichia phage EcSzw-2 (virus)
References: UniProt: A0A7C2VVZ8, citrate synthase (unknown stereospecificity)
#2: Chemical
ChemComp-CIT / CITRIC ACID / 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 / Water


Mass: 18.015 Da / Num. of mol.: 973 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Ammonium citrate tribasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 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: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.18→181.17 Å / Num. obs: 191541 / % possible obs: 97.5 % / Redundancy: 8.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.129 / Net I/σ(I): 32
Reflection shellResolution: 2.18→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
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ixe

1ixe


Resolution: 2.19→181.17 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.415 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 9674 5.1 %RANDOM
Rwork0.1957 ---
obs0.1984 181866 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.01 Å2 / Biso mean: 36.133 Å2 / Biso min: 13.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å2-0 Å2
2--0.26 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: final / Resolution: 2.19→181.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26496 0 104 973 27573
Biso mean--32.56 35.15 -
Num. residues----3364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01927252
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225896
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.97136953
X-RAY DIFFRACTIONr_angle_other_deg1.106359740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70153348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61623.6271180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39154556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.49115152
X-RAY DIFFRACTIONr_chiral_restr0.1180.23988
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02130444
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026064
LS refinement shellResolution: 2.19→2.245 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.289 728 -
Rwork0.235 13022 -
obs--93.98 %

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