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- PDB-7e8n: Crystal structure of Type II citrate synthase (HyCS) from Hymenob... -

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Basic information

Entry
Database: PDB / ID: 7e8n
TitleCrystal structure of Type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554
ComponentsCitrate synthase
KeywordsTRANSFERASE / citrate synthase / Hymenobacter sp. PAMC 26554 / domain movement / RIBOSOMAL PROTEIN
Function / homology
Function and homology information


: / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Citrate synthase, type I / Citrate synthase, bacterial-type / 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
Similarity search - Component
Biological speciesHymenobacter sp. PAMC 26554 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPark, S.-H. / Lee, C.W. / Bae, D.-W. / Lee, J.H.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Structural basis of the cooperative activation of type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554.
Authors: Park, S.H. / Lee, C.W. / Bae, D.W. / Do, H. / Jeong, C.S. / Hwang, J. / Cha, S.S. / Lee, J.H.
History
DepositionMar 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 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

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)145,6536
Polymers145,0773
Non-polymers5763
Water7,098394
1
A: Citrate synthase
B: Citrate synthase
C: Citrate synthase
hetero molecules

A: Citrate synthase
B: Citrate synthase
C: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,30712
Polymers290,1546
Non-polymers1,1536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area45140 Å2
ΔGint-220 kcal/mol
Surface area88660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.339, 166.168, 135.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-758-

HOH

21B-642-

HOH

31B-657-

HOH

41B-684-

HOH

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Components

#1: Protein Citrate synthase


Mass: 48358.984 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hymenobacter sp. PAMC 26554 (bacteria) / Gene: gltA, A0257_01235 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A142HAE2
#2: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate, HCl (pH 6.5), 1 M sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 76885 / % possible obs: 99.8 % / Redundancy: 7.9 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 47.2
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.342 / Num. unique obs: 3807

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVM

4tvm


Resolution: 2.2→41.58 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.851 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 3848 5 %RANDOM
Rwork0.19 ---
obs0.1923 72970 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.45 Å2 / Biso mean: 46.798 Å2 / Biso min: 14.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0 Å20 Å2
2---3.76 Å2-0 Å2
3---4.47 Å2
Refinement stepCycle: final / Resolution: 2.2→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10051 0 39 394 10484
Biso mean--59.66 41.78 -
Num. residues----1280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179717
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.64313985
X-RAY DIFFRACTIONr_angle_other_deg1.3261.57322430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18551274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67322.882510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.835151749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0141551
X-RAY DIFFRACTIONr_chiral_restr0.0750.21358
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022315
LS refinement shellResolution: 2.2→2.254 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.282 292 -
Rwork0.236 5237 -
obs--97.82 %

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