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- PDB-2ifc: The Structure of the Binary Complex of Oxalateacetate with Citrat... -

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Basic information

Entry
Database: PDB / ID: 2ifc
TitleThe Structure of the Binary Complex of Oxalateacetate with Citrate Synthase from the Thermophilic Archaeon Thermolasma acidophilum
ComponentsCitrate Synthase
KeywordsTRANSFERASE / Citrate synthase / Oxaloacetate / EC 2.3.3.1
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate (Si)-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 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
OXALOACETATE ION / Citrate synthase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLehmann, C.
CitationJournal: To be Published
Title: To be anounced
Authors: Lehmann, C. / Kurz, C. / Ellenberger, E.
History
DepositionSep 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)173,0338
Polymers172,5094
Non-polymers5244
Water40,1372228
1
A: Citrate Synthase
C: Citrate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5174
Polymers86,2552
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-38 kcal/mol
Surface area27390 Å2
MethodPISA, PQS
2
B: Citrate Synthase
D: Citrate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5174
Polymers86,2552
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-40 kcal/mol
Surface area26950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.526, 97.447, 106.937
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe Biological Assembly is a dimer. There are two Dimer in the AU.

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Components

#1: Protein
Citrate Synthase / E.C.2.3.3.1


Mass: 43127.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: gltA / Production host: Escherichia coli (E. coli) / References: UniProt: P21553, citrate (Si)-synthase
#2: Chemical
ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2228 / 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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 17 % PEG 4000, 100mM Hepes 8.5, 200mM Sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 14, 2006 / Details: Double crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→41.38 Å / Num. all: 170739 / Num. obs: 170738 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.19 % / Rmerge(I) obs: 0.09 / Χ2: 0.93 / Net I/σ(I): 10 / Scaling rejects: 21558
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.03 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.9 / Num. measured all: 100678 / Num. unique all: 16592 / Χ2: 1 / % possible all: 94.5

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Phasing

Phasing MR
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct98.5 0

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
CNSrefinement
d*TREK9.6LDzdata scaling
PDB_EXTRACT2data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O7X_A

Resolution: 1.7→41.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.457 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 8560 5 %RANDOM
Rwork0.181 ---
obs0.183 170707 96.77 %-
all-170707 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.348 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.05 Å2
2--0.11 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11958 0 36 2228 14222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02212327
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.96216667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56251530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61823.971549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.959152167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8641575
X-RAY DIFFRACTIONr_chiral_restr0.1210.21812
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029341
X-RAY DIFFRACTIONr_nbd_refined0.2110.27358
X-RAY DIFFRACTIONr_nbtor_refined0.3060.28731
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.21763
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.278
X-RAY DIFFRACTIONr_mcbond_it1.1081.57866
X-RAY DIFFRACTIONr_mcangle_it1.563212219
X-RAY DIFFRACTIONr_scbond_it2.61935208
X-RAY DIFFRACTIONr_scangle_it3.9214.54448
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 597 -
Rwork0.272 11672 -
obs-12269 94.22 %

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