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- PDB-5k87: crystal structure of malonate bound to methylaconitate isomerase ... -

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Basic information

Entry
Database: PDB / ID: 5k87
Titlecrystal structure of malonate bound to methylaconitate isomerase PrpF from Shewanella oneidensis
Components2-methyl-aconitate isomerase
KeywordsISOMERASE / PrpF methylaconitate isomerase 2-MMC
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
MALONATE ION / 2-methyl-aconitate isomerase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.219 Å
AuthorsRayment, I. / Wetterhorn, K.
CitationJournal: PLoS ONE / Year: 2017
Title: The PrpF protein of Shewanella oneidensis MR-1 catalyzes the isomerization of 2-methyl-cis-aconitate during the catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle.
Authors: Rocco, C.J. / Wetterhorn, K.M. / Garvey, G.S. / Rayment, I. / Escalante-Semerena, J.C.
History
DepositionMay 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-methyl-aconitate isomerase
B: 2-methyl-aconitate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9816
Polymers83,5732
Non-polymers4084
Water20,0511113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-6 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.825, 103.393, 78.088
Angle α, β, γ (deg.)90.00, 104.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2-methyl-aconitate isomerase / Cis-trans isomerase


Mass: 41786.348 Da / Num. of mol.: 2 / Mutation: K73E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: prpF, SO_0342 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8EJW4, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1113 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES pH 6.0, 136 mM sodium malonate, 15% polyethylene glycol 4000 (PEG 4K)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 227930 / % possible obs: 96.5 % / Redundancy: 13 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 49.5
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.4 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pvz

2pvz


Resolution: 1.219→31.36 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 10804 5.05 %Random selection
Rwork0.1628 ---
obs0.1638 213736 90.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.219→31.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 0 28 1113 6838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066047
X-RAY DIFFRACTIONf_angle_d1.088261
X-RAY DIFFRACTIONf_dihedral_angle_d12.1592194
X-RAY DIFFRACTIONf_chiral_restr0.069951
X-RAY DIFFRACTIONf_plane_restr0.0051105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2185-1.23240.28371180.23392166X-RAY DIFFRACTION29
1.2324-1.24690.25111550.23432942X-RAY DIFFRACTION40
1.2469-1.26210.26092100.23893932X-RAY DIFFRACTION52
1.2621-1.27810.27062810.23695180X-RAY DIFFRACTION70
1.2781-1.29490.24723380.2316282X-RAY DIFFRACTION84
1.2949-1.31260.2593530.22696736X-RAY DIFFRACTION92
1.3126-1.33140.23553640.22137098X-RAY DIFFRACTION94
1.3314-1.35130.23733580.21347097X-RAY DIFFRACTION95
1.3513-1.37240.20993650.20457209X-RAY DIFFRACTION96
1.3724-1.39490.20183700.20087302X-RAY DIFFRACTION97
1.3949-1.41890.21973580.19487241X-RAY DIFFRACTION97
1.4189-1.44470.23463830.18917275X-RAY DIFFRACTION97
1.4447-1.47250.20453850.18497233X-RAY DIFFRACTION97
1.4725-1.50260.19193680.18017299X-RAY DIFFRACTION97
1.5026-1.53520.19833940.18287274X-RAY DIFFRACTION97
1.5352-1.5710.19713680.17687236X-RAY DIFFRACTION96
1.571-1.61020.20583830.1737329X-RAY DIFFRACTION98
1.6102-1.65380.18513990.1717288X-RAY DIFFRACTION98
1.6538-1.70240.18664100.17387335X-RAY DIFFRACTION98
1.7024-1.75740.19024350.16917284X-RAY DIFFRACTION98
1.7574-1.82020.1783840.17027395X-RAY DIFFRACTION99
1.8202-1.89310.18823920.16537402X-RAY DIFFRACTION99
1.8931-1.97920.16063970.16837264X-RAY DIFFRACTION97
1.9792-2.08350.17524180.16077391X-RAY DIFFRACTION99
2.0835-2.2140.18364280.15767406X-RAY DIFFRACTION99
2.214-2.38490.18484050.16137444X-RAY DIFFRACTION99
2.3849-2.62480.18253850.16387475X-RAY DIFFRACTION99
2.6248-3.00440.18514290.16577362X-RAY DIFFRACTION98
3.0044-3.78420.16743700.14167532X-RAY DIFFRACTION100
3.7842-31.37050.14964010.13227523X-RAY DIFFRACTION98

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