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- PDB-3rga: Crystal structure of epoxide hydrolase for polyether lasalocid A ... -

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Basic information

Entry
Database: PDB / ID: 3rga
TitleCrystal structure of epoxide hydrolase for polyether lasalocid A biosynthesis
ComponentsEpoxide hydrolase
KeywordsISOMERASE / NTF2-like / Epoxide-opening cyclic ether formation
Function / homology
Function and homology information


Isomerases; Intramolecular lyases / antibiotic biosynthetic process / isomerase activity
Similarity search - Function
SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Chem-ILD / Chem-LSB / METHANOL / Epoxide hydrolase LasB / Epoxide hydrolase LasB
Similarity search - Component
Biological speciesStreptomyces lasaliensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 1.59 Å
AuthorsHotta, K. / Mathews, I.I. / Chen, X. / Kim, C.-Y.
CitationJournal: Nature / Year: 2012
Title: Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis
Authors: Hotta, K. / Chen, X. / Paton, R.S. / Minami, A. / Li, H. / Swaminathan, K. / Mathews, I.I. / Watanabe, K. / Oikawa, H. / Houk, K.N. / Kim, C.-Y.
History
DepositionApr 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,99913
Polymers30,4691
Non-polymers1,53112
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.850, 47.480, 62.330
Angle α, β, γ (deg.)90.00, 120.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Epoxide hydrolase /


Mass: 30468.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lasaliensis (bacteria) / Gene: lasB, lsd19 / Plasmid: pCold1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B5M9L7, UniProt: B6ZK72*PLUS, Hydrolases; Acting on ether bonds; Ether hydrolases

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Non-polymers , 8 types, 175 molecules

#2: Chemical ChemComp-LSB / (4R,5S)-3-[(2R,3S,4S)-2-ethyl-5-[(3R)-2-ethyl-3-[2-[(2R,3R)-2-ethyl-3-methyl-oxiran-2-yl]ethyl]oxiran-2-yl]-3-hydroxy-4-methyl-pentanoyl]-4-methyl-5-phenyl-1,3-oxazolidin-2-one


Mass: 501.655 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H43NO6
#3: Chemical ChemComp-ILD / (4R,5S)-3-[(2R)-2-{(2S,2'R,4S,5S,5'R)-2,5'-diethyl-5'-[(1S)-1-hydroxyethyl]-4-methyloctahydro-2,2'-bifuran-5-yl}butanoyl]-4-methyl-5-phenyl-1,3-oxazolidin-2-one


Mass: 501.655 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H43NO6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#7: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 1.6M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→29.45 Å / Num. all: 39256 / Num. obs: 39256 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.094 / Net I/σ(I): 12.2
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2827 / Rsym value: 0.941 / % possible all: 94.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLREP
Starting model: PDB Code 1E3V

1e3v


Resolution: 1.59→29.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.23 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19236 1966 5 %RANDOM
Rwork0.17261 ---
obs0.17362 37291 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.04 Å2
2--0.32 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.59→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 94 163 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022330
X-RAY DIFFRACTIONr_bond_other_d0.0020.021608
X-RAY DIFFRACTIONr_angle_refined_deg1.7812.0153183
X-RAY DIFFRACTIONr_angle_other_deg0.9763.0023858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.11521.73598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32515361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6211530
X-RAY DIFFRACTIONr_chiral_restr0.1030.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 132 -
Rwork0.292 2616 -
obs--96.12 %
Refinement TLS params.Method: refined / Origin x: 41.6734 Å / Origin y: 43.85 Å / Origin z: 7.684 Å
111213212223313233
T0.0118 Å2-0.0008 Å20.0071 Å2-0.0185 Å2-0.0048 Å2--0.0087 Å2
L1.1246 °20.1322 °20.2455 °2-0.8302 °20.1391 °2--1.3759 °2
S0.0278 Å °-0.0933 Å °0.0308 Å °0.0256 Å °0.0002 Å °-0.0359 Å °0.009 Å °0.098 Å °-0.028 Å °

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