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- PDB-4qa9: Ensemble refinement of an epoxide hydrolase from Streptomyces car... -

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Basic information

Entry
Database: PDB / ID: 4qa9
TitleEnsemble refinement of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus.
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / Epoxide hydrolase / PSI-Biology
Function / homology
Function and homology information


epoxide metabolic process / epoxide hydrolase activity / catabolic process
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
Biological speciesStreptomyces carzinostaticus subsp. neocarzinostaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsWang, F. / Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. ...Wang, F. / Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Joachimiak, A. / Phillips Jr., G.N. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: To be Published
Title: Ensemble refinement of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus.
Authors: Wang, F. / Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Joachimiak, A. / Phillips Jr., G.N.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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_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)44,35517
Polymers43,2261
Non-polymers1,12916
Water4,882271
1
A: Epoxide hydrolase
hetero molecules

A: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,71034
Polymers86,4522
Non-polymers2,25832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9250 Å2
ΔGint-65 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.330, 75.330, 165.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Number of models20
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

22A-505-

HOH

33A-683-

HOH

44A-567-

HOH

55A-545-

HOH

66A-533-

HOH

77A-524-

HOH

88A-516-

HOH

99A-510-

HOH

1010A-503-

HOH

1111A-619-

HOH

1212A-558-

HOH

1313A-542-

HOH

1414A-530-

HOH

1515A-521-

HOH

1616A-512-

HOH

1717A-506-

HOH

1818A-731-

HOH

1919A-568-

HOH

2020A-539-

HOH

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Components

#1: Protein Epoxide hydrolase


Mass: 43225.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces carzinostaticus subsp. neocarzinostaticus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q84HB8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 2.0M ammonium sulfate and 0.1M Tris:HCl, pH 8.5. Cyro was ethylene glycol., VAPOR DIFFUSION, temperature 298K

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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
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: 1.56→27.816 Å / Num. all: 66078 / Num. obs: 65946 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.56→1.59 Å / % possible all: 99.99

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1420refinement
PDB_EXTRACT3.14data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXPHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I19

4i19


Resolution: 1.56→27.816 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.151 3343 5.07 %same with 4i19
Rwork0.1219 ---
all0.1234 68419 --
obs0.1234 65942 96.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso min: 99999 Å2
Refinement stepCycle: LAST / Resolution: 1.56→27.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 68 271 3390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_plane_restr0.009
X-RAY DIFFRACTIONf_chiral_restr0.069
X-RAY DIFFRACTIONf_dihedral_angle_d9.95
X-RAY DIFFRACTIONf_angle_d1.216
X-RAY DIFFRACTIONf_bond_d0.009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5599-1.58210.22741200.2162162228282
1.5821-1.60570.221180.2022415253390
1.6057-1.63080.22851410.18462533267496
1.6308-1.65760.22191440.17392590273498
1.6576-1.68610.1941390.16712634277398
1.6861-1.71680.20171270.15052648277598
1.7168-1.74980.18481320.13262615274798
1.7498-1.78550.15641580.12092580273898
1.7855-1.82430.15791260.11512590271697
1.8243-1.86680.15161220.11152616273897
1.8668-1.91350.14141390.10852602274197
1.9135-1.96520.15641290.10812591272096
1.9652-2.0230.13621400.1032574271497
2.023-2.08830.13551310.10352648277996
2.0883-2.16290.13161350.09892568270396
2.1629-2.24940.13691290.0952585271496
2.2494-2.35180.12761480.09632567271595
2.3518-2.47570.10591540.09062620277497
2.4757-2.63070.14581580.09772604276296
2.6307-2.83360.14071600.1082632279297
2.8336-3.11840.1521450.12532736288199
3.1184-3.56890.17441480.13782758290699
3.5689-4.49330.15711520.12127882940100
4.4933-27.82080.13221480.14042943309199

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