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- PDB-2h12: Structure of Acetobacter aceti citrate synthase complexed with ox... -

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Basic information

Entry
Database: PDB / ID: 2h12
TitleStructure of Acetobacter aceti citrate synthase complexed with oxaloacetate and carboxymethyldethia coenzyme A (CMX)
ComponentsCitrate synthase
KeywordsTRANSFERASE / acidophile / citrate synthase / acetic acid resistance / allostery
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Rubrerythrin, domain 2 - #60 / 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 ...Rubrerythrin, domain 2 - #60 / 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 / Rubrerythrin, domain 2 / Single Sheet / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CARBOXYMETHYLDETHIA COENZYME *A / OXALOACETATE ION / Citrate synthase
Similarity search - Component
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStarks, C.M. / Kappock, T.J.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of a NADH-insensitive hexameric citrate synthase that resists acid inactivation.
Authors: Francois, J.A. / Starks, C.M. / Sivanuntakorn, S. / Jiang, H. / Ransome, A.E. / Nam, J.W. / Constantine, C.Z. / Kappock, T.J.
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence According to authors these are sequencing errors.

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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
E: Citrate synthase
F: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,56259
Polymers289,0766
Non-polymers9,48653
Water58,1703229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.660, 125.690, 150.590
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 / / Acetic acid resistance protein


Mass: 48179.316 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti (bacteria) / Strain: 1023 / Gene: aarA / Plasmid: pTWIN1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P20901, citrate (Si)-synthase
#2: Chemical
ChemComp-OAA / OXALOACETATE ION / Oxaloacetic acid


Mass: 131.064 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CMX / CARBOXYMETHYLDETHIA COENZYME *A


Mass: 793.505 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O18P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3229 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence According to authors these are sequencing errors

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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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 2.1 M ammonium sulfate, 150 mM sodium potassium tartrate, 35 mM sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 25, 2005 / Details: Rosenbaum-Rock monochromator
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→39.28 Å / Num. obs: 274629 / % possible obs: 100 % / Redundancy: 7.13 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.09 / Net I/σ(I): 8.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 27183 / Rsym value: 0.491 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
JBluIce-EPICSdata collection
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AJ8

1aj8


Resolution: 1.85→39.28 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 4147400.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 13558 5 %RANDOM
Rwork0.195 ---
all0.195 274629 --
obs0.195 273519 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.9305 Å2 / ksol: 0.388013 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.9 Å20 Å20 Å2
2--2.55 Å20 Å2
3---3.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19727 0 565 3229 23521
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.301 1342 4.9 %
Rwork0.263 25819 -
obs-27183 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3cmx_prodg.paramcmx_prodg.top
X-RAY DIFFRACTION4oaa_prodg.paramoaa_prodg.top
X-RAY DIFFRACTION5sulfate.paramsulfate.top

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