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- PDB-4meb: Crystal structure of aCif-D158S -

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Basic information

Entry
Database: PDB / ID: 4meb
TitleCrystal structure of aCif-D158S
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 / PHOSPHATE ION / :
Function and homology information
Biological speciesAcinetobacter sp. RUH2624 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBridges, A.A. / Bahl, 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 ...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

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Assembly

Deposited unit
A: Predicted protein
B: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0376
Polymers73,6602
Non-polymers3774
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-44 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.109, 42.511, 86.907
Angle α, β, γ (deg.)90.00, 98.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Predicted protein / Protein structure prediction


Mass: 36829.848 Da / Num. of mol.: 2 / Fragment: UNP residues 25-349 / Mutation: D158S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. RUH2624 (bacteria) / Gene: HMPREF0014_00517, ZP_05823503 / Plasmid: pMQ70 / Production host: Escherichia coli (E. coli) / References: UniProt: D0BWK6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 250 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: Feb 25, 2012 / 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: 2→40.85 Å / Num. obs: 40969 / % possible obs: 96 %

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MEA

4mea


Resolution: 2→40.85 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 17.18 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 2057 5.02 %thin shells
Rwork0.1547 ---
obs0.1568 40962 96.04 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.383 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7981 Å2-0 Å2-2.1153 Å2
2---0.6437 Å2-0 Å2
3----0.1544 Å2
Refinement stepCycle: LAST / Resolution: 2→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5064 0 21 562 5647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075298
X-RAY DIFFRACTIONf_angle_d1.0277186
X-RAY DIFFRACTIONf_dihedral_angle_d11.7721955
X-RAY DIFFRACTIONf_chiral_restr0.078752
X-RAY DIFFRACTIONf_plane_restr0.005925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.24181430.18332643X-RAY DIFFRACTION98
2.0465-2.09770.24361710.17662568X-RAY DIFFRACTION98
2.0977-2.15440.25251050.16672672X-RAY DIFFRACTION98
2.1544-2.21780.23561120.15892641X-RAY DIFFRACTION98
2.2178-2.28940.18892030.15662560X-RAY DIFFRACTION98
2.2894-2.37120.24261130.14972671X-RAY DIFFRACTION98
2.3712-2.46620.18641080.15632645X-RAY DIFFRACTION98
2.4662-2.57840.20991890.15282538X-RAY DIFFRACTION97
2.5784-2.71430.19181240.16142620X-RAY DIFFRACTION97
2.7143-2.88430.21051000.16012625X-RAY DIFFRACTION96
2.8843-3.10690.19531770.15792555X-RAY DIFFRACTION96
3.1069-3.41950.20891270.15972561X-RAY DIFFRACTION95
3.4195-3.91390.1627990.13612612X-RAY DIFFRACTION94
3.9139-4.92980.15031970.11582451X-RAY DIFFRACTION92
4.9298-40.8580.1942890.18132543X-RAY DIFFRACTION88
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)
10.25430.06650.07250.41640.18980.47490.01990.0410.0098-0.00190.0118-0.0342-0.03880.0323-0.01890.03590.00730.00670.00960.00520.0255-35.5518-10.0658-20.0123
20.61680.09440.07480.41340.06080.4143-0.005-0.01610.01650.0219-0.0330.0854-0.0159-0.05940.02320.0390.0298-0.01420.0769-0.02730.0558-72.9692-20.4373-23.9949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 25:348)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 25:348)

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