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- PDB-4mea: Crystal structure of the Cif epoxide hydrolase from Acinetobacter... -

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Basic information

Entry
Database: PDB / ID: 4mea
TitleCrystal structure of the Cif epoxide hydrolase from Acinetobacter nosocomialis
ComponentsPredicted proteinProtein structure prediction
KeywordsHYDROLASE / alpha/beta hydrolase fold / epoxide hydrolase / secreted
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesAcinetobacter sp. RUH2624 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBahl, C.D. / Madden, D.R.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Signature motifs identify an acinetobacter cif virulence factor with epoxide hydrolase activity.
Authors: Bahl, C.D. / Hvorecny, K.L. / Bridges, A.A. / Ballok, A.E. / Bomberger, J.M. / Cady, K.C. / O'Toole, G.A. / Madden, D.R.
History
DepositionAug 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references / 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
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: Predicted protein
B: Predicted protein


Theoretical massNumber of molelcules
Total (without water)73,7162
Polymers73,7162
Non-polymers00
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-19 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.688, 42.584, 86.470
Angle α, β, γ (deg.)90.00, 98.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Predicted protein / Protein structure prediction


Mass: 36857.859 Da / Num. of mol.: 2 / Fragment: UNP residues 25-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. RUH2624 (bacteria) / Gene: acif, HMPREF0014_00517 / Plasmid: pMQ70 / Production host: Escherichia coli (E. coli) / References: UniProt: D0BWK6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100 mM monopotassium phosphate, 100 mM sodium citrate, 20% PEG 4000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 27, 2011 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→42.42 Å / Num. obs: 45537 / % possible obs: 99.8 %

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KD2

3kd2


Resolution: 1.95→42.417 Å / SU ML: 0.19 / σ(F): 2.01 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 2296 5.04 %thin shells
Rwork0.1456 ---
obs0.1476 45523 99.79 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.288 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7791 Å2-0 Å2-3.1777 Å2
2---0.4562 Å2-0 Å2
3----0.3228 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5059 0 0 608 5667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075245
X-RAY DIFFRACTIONf_angle_d1.0287112
X-RAY DIFFRACTIONf_dihedral_angle_d11.6851924
X-RAY DIFFRACTIONf_chiral_restr0.075747
X-RAY DIFFRACTIONf_plane_restr0.005916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99240.25521350.17442667X-RAY DIFFRACTION100
1.9924-2.03870.21071740.15862653X-RAY DIFFRACTION100
2.0387-2.08970.24331530.14592657X-RAY DIFFRACTION100
2.0897-2.14620.19441160.14822712X-RAY DIFFRACTION100
2.1462-2.20940.21531150.14952698X-RAY DIFFRACTION100
2.2094-2.28070.20311620.14072686X-RAY DIFFRACTION100
2.2807-2.36220.19561850.14222643X-RAY DIFFRACTION100
2.3622-2.45670.19181140.14292709X-RAY DIFFRACTION100
2.4567-2.56850.2061170.14862703X-RAY DIFFRACTION100
2.5685-2.70390.18091150.14722728X-RAY DIFFRACTION100
2.7039-2.87330.18112330.14642614X-RAY DIFFRACTION100
2.8733-3.09510.18291150.14042744X-RAY DIFFRACTION100
3.0951-3.40640.17861130.14622726X-RAY DIFFRACTION100
3.4064-3.89910.15921130.13072780X-RAY DIFFRACTION100
3.8991-4.91120.14232290.11872644X-RAY DIFFRACTION100
4.9112-42.42660.22641070.1852863X-RAY DIFFRACTION99
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)
10.00640.00160.00330.00410.00040.0039-0.00260.00330.00780.0051-0.0058-0.0111-0.00660.007-0.02160.0238-0.013-0.01120.03030.01460.0259-6.72485.6928-18.9426
20.0137-0.00640.00680.0113-0.00750.00560.0031-0.0049-0.00230.00140.00140.0052-0.0017-0.00290.00060.0154-0.00360.00440.00650.00010.0078-44.29216.4001-22.7176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 25:348)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 26:348)

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