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- PDB-1iom: CRYSTAL STRUCTURE OF CITRATE SYNTHASE FROM THERMUS THERMOPHILUS HB8 -

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Basic information

Entry
Database: PDB / ID: 1iom
TitleCRYSTAL STRUCTURE OF CITRATE SYNTHASE FROM THERMUS THERMOPHILUS HB8
ComponentsCITRATE SYNTHASE
KeywordsLYASE / Open Form / synthase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


citrate synthase activity / tricarboxylic acid cycle / 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-like, large alpha subdomain / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain ...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-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBONATE ION / Citrate synthase / Citrate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKanamori, E. / 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
DepositionMar 19, 2001Deposition 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: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 4, 2015Group: Database references
Revision 1.5Jan 1, 2020Group: Advisory / Database references / Category: citation / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.6Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7956
Polymers42,3621
Non-polymers4325
Water8,449469
1
A: CITRATE SYNTHASE
hetero molecules

A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,59012
Polymers84,7252
Non-polymers86510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11230 Å2
ΔGint-48 kcal/mol
Surface area26210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.55, 84.55, 153.52
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1262-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: y, x, -z.

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Components

#1: Protein CITRATE SYNTHASE


Mass: 42362.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSE
References: UniProt: Q9LCX9, UniProt: Q5SIM6*PLUS, 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-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44B210.7
SYNCHROTRONSPring-8 BL41XU2
Detector
TypeIDDetectorDate
MARRESEARCH1CCDDec 9, 1999
2Nov 19, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 86558 / Num. obs: 86558 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.6 / Num. unique all: 12907 / % possible all: 100

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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: PDB ENTRY 1AJ8

1aj8


Resolution: 1.5→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.185 8685 10 %RANDOM
Rwork0.172 ---
all0.172 86558 --
obs0.172 86558 96.6 %-
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 27 469 3425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.004
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.213 1392 -
Rwork0.186 --
obs-14648 100 %

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