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- PDB-2ibp: Crystal Structure of Citrate Synthase from Pyrobaculum aerophilum -

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Basic information

Entry
Database: PDB / ID: 2ibp
TitleCrystal Structure of Citrate Synthase from Pyrobaculum aerophilum
ComponentsCitrate synthase
KeywordsTRANSFERASE / DISULFIDE BOND / HOMODIMER / CITRATE SYNTHASE / THERMOPHILIC / CATENANE
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / 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
ACETATE ION / Citrate synthase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBoutz, D.R. / Yeates, T.O. / Cascio, D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Discovery of a thermophilic protein complex stabilized by topologically interlinked chains.
Authors: Boutz, D.R. / Cascio, D. / Whitelegge, J. / Perry, L.J. / Yeates, T.O.
History
DepositionSep 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0496
Polymers92,8822
Non-polymers1674
Water14,556808
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
ΔGint-81 kcal/mol
Surface area30120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.418, 89.803, 146.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Citrate synthase


Mass: 46441.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: IM2 / Gene: PAE1689 / Plasmid: PETM11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZWP2, citrate (Si)-synthase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.1M Sodium cacodylate trihydrate pH 6.5, 0.2M Magnesium acetate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2005 / Details: Mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→76.47 Å / Num. all: 107121 / Num. obs: 107121 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 22.9 Å2 / Rsym value: 0.085 / Net I/σ(I): 21.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 9959 / Rsym value: 0.686 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BOSV. 1.0data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VGP

1vgp


Resolution: 1.6→76.47 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.381 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18975 5286 5 %RANDOM
Rwork0.15769 ---
all0.15929 100651 --
obs0.15929 100651 94.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.086 Å0.085 Å
Refinement stepCycle: LAST / Resolution: 1.6→76.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 10 808 7346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226822
X-RAY DIFFRACTIONr_bond_other_d0.0010.024757
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9669267
X-RAY DIFFRACTIONr_angle_other_deg0.813.00111513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3035842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6822.716324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.834151157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1061558
X-RAY DIFFRACTIONr_chiral_restr0.0930.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021479
X-RAY DIFFRACTIONr_nbd_refined0.2190.21709
X-RAY DIFFRACTIONr_nbd_other0.2050.25487
X-RAY DIFFRACTIONr_nbtor_refined0.1930.23525
X-RAY DIFFRACTIONr_nbtor_other0.0880.23378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2679
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.30625377
X-RAY DIFFRACTIONr_mcbond_other0.96821647
X-RAY DIFFRACTIONr_mcangle_it4.30636632
X-RAY DIFFRACTIONr_scbond_it5.3623216
X-RAY DIFFRACTIONr_scangle_it7.40332620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 363 -
Rwork0.236 6756 -
obs--87.27 %

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