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- PDB-4i19: The crystal structure of an epoxide hydrolase from Streptomyces c... -

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Basic information

Entry
Database: PDB / ID: 4i19
TitleThe crystal structure of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus.
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesi / NatPro / Enzyme Discovery for Natural Product Biosynthesis
Function / homology
Function and homology information


ether hydrolase activity
Similarity search - Function
Epoxide hydrolase, N-terminal / Epoxide hydrolase N terminus / Epoxide hydrolase / Epoxide hydrolase-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Epoxide hydrolase
Similarity search - Component
Biological speciesStreptomyces carzinostaticus subsp. neocarzinostaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.148 Å
AuthorsTan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: To be Published
Title: The crystal structure of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus.
Authors: Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A.
History
DepositionNov 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Structure summary
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,32013
Polymers43,7421
Non-polymers57812
Water3,441191
1
A: Epoxide hydrolase
hetero molecules

A: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,64026
Polymers87,4842
Non-polymers1,15724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area9690 Å2
ΔGint-26 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.011, 76.011, 161.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

DetailsExperimentally unknonw. The chain A may form a dimer with it symmetry-related molecule thorugh the operator (-y,-x,-z+1/2).

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Components

#1: Protein Epoxide hydrolase


Mass: 43741.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces carzinostaticus subsp. neocarzinostaticus (bacteria)
Strain: subsp. neocarzinostaticus / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q84HB8
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.4M Sodium Malonate, 0.1M Bis-Tris Propane:NaOH, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2012 / Details: mirror
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.148→33.5 Å / Num. all: 26537 / Num. obs: 26537 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 31.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1275 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.148→33.262 Å / SU ML: 0.5 / σ(F): 1.34 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1335 5.05 %random
Rwork0.1624 ---
all0.1648 26457 --
obs0.1648 26457 99.56 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.849 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.7538 Å2-0 Å20 Å2
2---7.7538 Å2-0 Å2
3---15.5075 Å2
Refinement stepCycle: LAST / Resolution: 2.148→33.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 38 191 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073145
X-RAY DIFFRACTIONf_angle_d1.044269
X-RAY DIFFRACTIONf_dihedral_angle_d13.6851134
X-RAY DIFFRACTIONf_chiral_restr0.066460
X-RAY DIFFRACTIONf_plane_restr0.005558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1482-2.2250.23251160.18892403X-RAY DIFFRACTION97
2.225-2.31410.27471380.18812457X-RAY DIFFRACTION100
2.3141-2.41940.23631180.17142473X-RAY DIFFRACTION100
2.4194-2.54690.21051280.17442519X-RAY DIFFRACTION100
2.5469-2.70640.23691350.18072475X-RAY DIFFRACTION100
2.7064-2.91520.30061440.19332499X-RAY DIFFRACTION100
2.9152-3.20840.26131460.19362487X-RAY DIFFRACTION100
3.2084-3.67210.21311460.16222508X-RAY DIFFRACTION100
3.6721-4.62450.14591310.12632566X-RAY DIFFRACTION99
4.6245-33.26620.17491330.15222735X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.68190.38211.3265.90886.13666.89510.15540.2361-0.29850.63370.467-0.52940.82120.8157-0.64890.30620.0565-0.07470.3663-0.06020.482227.0171-7.590751.1158
23.74150.68332.26742.38440.41652.51760.07690.5173-0.1786-0.18190.0738-0.40610.06940.5207-0.22010.3052-0.01270.04270.3783-0.09490.296617.5161-5.717529.5548
31.62740.53390.7592.1630.49610.91290.0715-0.0123-0.08980.1344-0.0234-0.08450.03360.0341-0.03180.18460.0087-0.02010.266-0.05780.230923.012510.430456.5378
42.8158-0.25111.26481.8846-0.5443.1736-0.0207-0.0560.1612-0.09850.10120.1126-0.1648-0.1096-0.02530.214-0.00990.02130.1913-0.02520.30086.010720.920250.257
51.22-0.02950.11250.924-0.09540.17110.02660.0547-0.036-0.04950.0489-0.08080.02630.0397-0.08430.2646-0.0055-0.03490.2809-0.05670.225110.23746.110744.3114
63.6493-0.64120.15752.08160.36421.37310.06590.04280.4137-0.0844-0.0463-0.1229-0.24770.0764-0.03080.2733-0.04730.01280.2559-0.03110.331915.619926.121847.9677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:21)
2X-RAY DIFFRACTION2chain 'A' and (resseq 22:51)
3X-RAY DIFFRACTION3chain 'A' and (resseq 52:162)
4X-RAY DIFFRACTION4chain 'A' and (resseq 163:230)
5X-RAY DIFFRACTION5chain 'A' and (resseq 231:339)
6X-RAY DIFFRACTION6chain 'A' and (resseq 340:385)

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