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- PDB-1vgm: Crystal Structure of an Isozyme of Citrate Synthase from Sulfolbu... -

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Basic information

Entry
Database: PDB / ID: 1vgm
TitleCrystal Structure of an Isozyme of Citrate Synthase from Sulfolbus tokodaii strain7
Components378aa long hypothetical citrate synthase
KeywordsTRANSFERASE / Open Form
Function / homology
Function and homology information


citrate synthase activity / citrate synthase (unknown stereospecificity) / tricarboxylic acid cycle / membrane => GO:0016020 / cytoplasm
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 active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase ...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 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMurakami, M. / Ihara, K. / Kouyama, T.
CitationJournal: Biochem Res Int / Year: 2016
Title: Crystal Structures of Two Isozymes of Citrate Synthase from Sulfolobus tokodaii Strain 7.
Authors: Murakami, M. / Kouyama, T.
History
DepositionApr 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: 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 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 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: 378aa long hypothetical citrate synthase
B: 378aa long hypothetical citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6244
Polymers85,4362
Non-polymers1882
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-68 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.870, 94.170, 77.620
Angle α, β, γ (deg.)90.00, 97.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homodimer in the asymmetric unit.

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Components

#1: Protein 378aa long hypothetical citrate synthase


Mass: 42718.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Gene: strain7 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q96ZM7, citrate (Si)-synthase, EC: 4.1.3.7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium Sulfate, HEPES, PEG400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2003 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30.3 Å / Num. all: 88582 / Num. obs: 57694 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 5.5 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.8 / Num. unique all: 7956 / % possible all: 97.1

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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: 1O7X

1o7x


Resolution: 2→30.3 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms 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
Rfree0.231 5778 10.2 %RANDOM
Rwork0.196 ---
obs0.196 57694 --
all-88582 --
Displacement parametersBiso mean: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20.56 Å2
2--0.3 Å20 Å2
3----1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 11 341 6346
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg0.9
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d21.2
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d0.74
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.841.5
X-RAY DIFFRACTIONo_mcangle_it2.382
X-RAY DIFFRACTIONo_scbond_it2.922
X-RAY DIFFRACTIONo_scangle_it3.92.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 5778 10.2 %
Rwork0.212 8479 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_1.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2WATER_REP.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3GOL.PARAM&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4ION.PARAM&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_TOPOLOGY_INFILE_5

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