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- PDB-3wmd: Crystal structure of epoxide hydrolase MonBI -

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Basic information

Entry
Database: PDB / ID: 3wmd
TitleCrystal structure of epoxide hydrolase MonBI
ComponentsProbable monensin biosynthesis isomerase
KeywordsISOMERASE / NTF2-like / Epoxide-opening cyclic ether formation
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / isomerase activity / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / MonBI
Function and homology information
Biological speciesStreptomyces cinnamonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.999 Å
AuthorsMinami, A. / Ose, T. / Sato, K. / Oikawa, A. / Kuroki, K. / Maenaka, K. / Oguri, H. / Oikawa, H.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Allosteric regulation of epoxide opening cascades by a pair of epoxide hydrolases in monensin biosynthesis
Authors: Minami, A. / Ose, T. / Sato, K. / Oikawa, A. / Kuroki, K. / Maenaka, K. / Oguri, H. / Oikawa, H.
History
DepositionNov 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Experimental preparation
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable monensin biosynthesis isomerase
B: Probable monensin biosynthesis isomerase


Theoretical massNumber of molelcules
Total (without water)35,6172
Polymers35,6172
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-10 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.784, 56.610, 106.973
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 Probable monensin biosynthesis isomerase


Mass: 17808.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cinnamonensis (bacteria) / Gene: monBI / Plasmid: pColdI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q846W7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.65 Å3/Da / Density % sol: 25.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1M potassium phosphate, 20%(v/v) PEG6000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.000, 0.9300, 0.9797
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 4, 2012 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.931
30.97971
ReflectionResolution: 1.999→50 Å / Num. obs: 16242 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 39
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.2 / Num. unique all: 676 / % possible all: 83.9

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.999→31.398 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 31.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 798 4.94 %RANDOM
Rwork0.2169 ---
obs0.2194 16143 97.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→31.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 0 98 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052298
X-RAY DIFFRACTIONf_angle_d1.1233130
X-RAY DIFFRACTIONf_dihedral_angle_d13.849850
X-RAY DIFFRACTIONf_chiral_restr0.061350
X-RAY DIFFRACTIONf_plane_restr0.006411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.999-2.12420.38281280.3038221287
2.1242-2.28820.3721430.2735252698
2.2882-2.51840.27571070.25872593100
2.5184-2.88260.33821370.23582618100
2.8826-3.63090.2571480.2042624100
3.6309-31.4020.20891350.192772100

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