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- PDB-1ixe: Crystal structure of citrate synthase from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1ixe
TitleCrystal structure of citrate synthase from Thermus thermophilus HB8
Componentscitrate synthase
KeywordsLYASE / enzyme-products complex / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


citrate synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily ...2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / COENZYME A / Citrate synthase / Citrate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMurakami, M. / Kanamori, E. / Kawaguchi, S. / Kuramitsu, S. / Kouyama, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biophys Physicobio. / Year: 2015
Title: Structural comparison between the open and closed forms of citrate synthase from Thermus thermophilus HB8.
Authors: Kanamori, E. / Kawaguchi, S. / Kuramitsu, S. / Kouyama, T. / Murakami, M.
History
DepositionJun 20, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Nov 4, 2015Group: Database references
Revision 1.5Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.6Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,61726
Polymers169,4504
Non-polymers5,16822
Water9,314517
1
A: citrate synthase
B: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,30913
Polymers84,7252
Non-polymers2,58411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13650 Å2
ΔGint-90 kcal/mol
Surface area25380 Å2
MethodPISA
2
C: citrate synthase
D: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,30913
Polymers84,7252
Non-polymers2,58411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-83 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.010, 110.630, 184.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer generated from the monomer in the asymmetric unit by the operations: y, x, -z.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
citrate synthase


Mass: 42362.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LCX9, UniProt: Q5SIM6*PLUS, EC: 4.1.3.7

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Non-polymers , 5 types, 539 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: lithium sulfate, sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 28, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→24.12 Å / Num. all: 73387 / Num. obs: 66309 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.4 / Num. unique all: 8335 / Rsym value: 0.217 / % possible all: 76.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IOM

1iom


Resolution: 2.3→14.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1489795.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 6728 10.1 %RANDOM
Rwork0.177 ---
all0.179 73387 --
obs0.179 66309 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.8 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---3.95 Å20 Å2
3---2.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.3→14.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11617 0 318 517 12452
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 942 10.2 %
Rwork0.186 8320 -
obs--76.7 %

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