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- PDB-2pw0: crystal structure of trans-aconitate bound to methylaconitate iso... -

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Basic information

Entry
Database: PDB / ID: 2pw0
Titlecrystal structure of trans-aconitate bound to methylaconitate isomerase PrpF from Shewanella oneidensis
ComponentsPrpF methylaconitate isomerase
KeywordsUNKNOWN FUNCTION / propionate catabolism / diaminopimelate epimerase like / aconitate binding
Function / homology
Function and homology information


intramolecular oxidoreductase activity, transposing C=C bonds / propionate catabolic process, 2-methylcitrate cycle / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
Similarity search - Function
2-methyl-aconitate isomerase PrpF / PrpF protein / PrpF protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
TRICARBALLYLIC ACID / 2-methyl-aconitate isomerase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsGarvey, G.S. / Rayment, I.R.
CitationJournal: Protein Sci. / Year: 2007
Title: The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: insights into its biological function.
Authors: Garvey, G.S. / Rocco, C.J. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionMay 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: PrpF methylaconitate isomerase
B: PrpF methylaconitate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,12910
Polymers83,4052
Non-polymers7258
Water15,853880
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PrpF methylaconitate isomerase
hetero molecules

B: PrpF methylaconitate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,12910
Polymers83,4052
Non-polymers7258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6700 Å2
ΔGint2 kcal/mol
Surface area26600 Å2
MethodPISA
3
A: PrpF methylaconitate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0655
Polymers41,7021
Non-polymers3624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: PrpF methylaconitate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0655
Polymers41,7021
Non-polymers3624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.879, 104.054, 78.212
Angle α, β, γ (deg.)90.00, 103.85, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homodimer. There is one homodimer in the asymetric unit.

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Components

#1: Protein PrpF methylaconitate isomerase


Mass: 41702.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: PrpF / Plasmid: pPRP196 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8EJW4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TRC / TRICARBALLYLIC ACID


Mass: 176.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19% methyl ether poly(ethyleneglycol) 5000 buffered with N-(2-hydroxyethyl)-piperazine-N9-2-ethanesulfonic acid (HEPES) buffer (100 mM, pH 7.5 at 25 C)., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.964107 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964107 Å / Relative weight: 1
ReflectionResolution: 1.57→76.03 Å / Num. all: 463390 / Num. obs: 463390 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.25
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6264 / % possible all: 88.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-CollectCOLLECTdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→76.03 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.662 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23208 5191 5 %RANDOM
Rwork0.20223 ---
obs0.20372 98622 92.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.598 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.4 Å2
2--0.32 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.57→76.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 48 880 6226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225490
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.967465
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39624.126206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63915834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4171530
X-RAY DIFFRACTIONr_chiral_restr0.0830.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024168
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.22698
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23807
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2716
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.260
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6891.53690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0425796
X-RAY DIFFRACTIONr_scbond_it1.69131979
X-RAY DIFFRACTIONr_scangle_it2.5374.51661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 320 -
Rwork0.266 6264 -
obs-6264 80.16 %

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