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- PDB-1ehy: X-ray structure of the epoxide hydrolase from agrobacterium radio... -

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Basic information

Entry
Database: PDB / ID: 1ehy
TitleX-ray structure of the epoxide hydrolase from agrobacterium radiobacter ad1
ComponentsPROTEIN (SOLUBLE EPOXIDE HYDROLASE)
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD / EPOXIDE DEGRADATION / EPICHLOROHYDRIN
Function / homology
Function and homology information


epoxide hydrolase / hydrolase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Epoxide hydrolase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsNardini, M. / Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Rink, R. / Janssen, D.B. / Dijkstra, B.W.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: The x-ray structure of epoxide hydrolase from Agrobacterium radiobacter AD1. An enzyme to detoxify harmful epoxides.
Authors: Nardini, M. / Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Rink, R. / Janssen, D.B. / Dijkstra, B.W.
#1: Journal: Tetrahedron / Year: 1998
Title: Enantioselectivity of a Recombinant Epoxide Hydrolase from Agrobacterium Radiobacter
Authors: Lutje Spelberg, J.H. / Rink, R. / Kellogg, R.M. / Janssen, D.B.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: Primary Structure and Catalytic Mechanism of the Epoxide Hydrolase from Agrobacterium Radiobacter AD1
Authors: Rink, R. / Fennema, M. / Smids, M. / Dehmel, U. / Janssen, D.B.
#3: Journal: Biochemistry / Year: 1998
Title: Kinetic Mechanism of the Enantioselective Conversion of Styrene Oxide by Epoxide Hydrolase from Agrobacterium Radiodacter AD1
Authors: Jacobs, M.H.J. / Van Den Wijngaard, A.J. / Pentenga, M. / Janssen, D.B.
#4: Journal: To be Published
Title: Mutation of Tyrosine Residues Involved in the Alkylation Half Reaction of Epoxide Hydrolase from Agrobacterium Radiodacter AD1 Results in Improved Enantioselectivity
Authors: Rink, R. / Lutje Spelberg, J.H. / Pieters, R.J. / Kingma, J. / Nardini, M. / Kellogg, R.M. / Dijkstra, B.W. / Janssen, D.B.
History
DepositionOct 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
B: PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
C: PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
D: PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4558
Polymers136,2994
Non-polymers1564
Water10,395577
1
A: PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1142
Polymers34,0751
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1142
Polymers34,0751
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1142
Polymers34,0751
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1142
Polymers34,0751
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.624, 100.201, 96.879
Angle α, β, γ (deg.)90.00, 100.68, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6101, 0.6478, -0.4562), (0.6611, 0.0989, -0.7437), (-0.4367, -0.7553, -0.4886)47.7899, 71.063, 144.7527
2given(-0.0429, 0.1032, 0.9937), (0.1275, -0.986, 0.1078), (0.9909, 0.1313, 0.0292)-48.0912, 62.6696, 38.9836
3given(-0.3615, -0.7593, -0.5411), (-0.7267, -0.1341, 0.6737), (-0.5841, 0.6368, -0.5033)104.0244, 16.7175, 94.624

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Components

#1: Protein
PROTEIN (SOLUBLE EPOXIDE HYDROLASE)


Mass: 34074.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: AD1 / Plasmid: PGELAF+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O31243, soluble epoxide hydrolase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDUE TO A CRYSTAL CONTACT BETWEEN LOOP RESIDUES 246-251 OF MONOMERS C AND D AND MONOMERS A AND B, IN ...DUE TO A CRYSTAL CONTACT BETWEEN LOOP RESIDUES 246-251 OF MONOMERS C AND D AND MONOMERS A AND B, IN ALL 4 MONOMERS THE CATALYTIC ASP 246 IS PULLED OUT FROM THE ACTIVE SITE, SO ALLOWING RESIDUE GLN 134 TO MOVE INTO THE ACTIVE SITE.

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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: 2.57 Å3/Da / Density % sol: 52 %
Crystal growpH: 7 / Details: 1.8 M KH2PO4/K2HPO4, pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
21.6-1.8 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 73445 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.57 / % possible all: 82
Reflection
*PLUS
Num. measured all: 222880
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT CORRECTION USED DURING THE REFINEMENT IN ALL 4 MOLECULES IN THE ASYMMETRIC UNIT THE LOOP 246-251 SHOWS POOR ELECTRON DENSITY. HOWEVER CLEAR ELECTRON DENSITY IS PRESENT FOR THE ...Details: BULK SOLVENT CORRECTION USED DURING THE REFINEMENT IN ALL 4 MOLECULES IN THE ASYMMETRIC UNIT THE LOOP 246-251 SHOWS POOR ELECTRON DENSITY. HOWEVER CLEAR ELECTRON DENSITY IS PRESENT FOR THE SS BOND BETWEEN RESIDUES C248 AND D248. DUE TO A SLIGHTLY DIFFERENT CONFORMATION OF THAT LOOP IN MONOMER A, NO SS BOND IS OBSERVED BETWEEN RESIDUES A248 AND B248
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3544 5.2 %SHELLS
Rwork0.19 ---
obs0.19 68692 91.5 %-
Displacement parametersBiso mean: 28.3 Å2
Refine analyze
ObsFree
Luzzati d res low5 Å-
Luzzati sigma a0.29 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9262 0 4 577 9843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_improper_angle_d1.17
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.1→2.16 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.318 214 4.5 %
Rwork0.286 4538 -
obs--71.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.WATTOPH19.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5.2 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.318 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.286

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