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- PDB-1m33: Crystal Structure of BioH at 1.7 A -

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Basic information

Entry
Database: PDB / ID: 1m33
TitleCrystal Structure of BioH at 1.7 A
ComponentsBioH protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-betta-alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


pimelyl-[acyl-carrier protein] methyl ester esterase activity / pimelyl-[acyl-carrier protein] methyl ester esterase / biotin biosynthetic process / carboxylic ester hydrolase activity / cytoplasm
Similarity search - Function
Pimeloyl-[acyl-carrier protein] methyl ester esterase / 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
3-HYDROXY-PROPANOIC ACID / Pimeloyl-[acyl-carrier protein] methyl ester esterase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsSanishvili, R. / Savchenko, A. / Skarina, T. / Edwards, A. / Joachimiak, A. / Yakunin, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli.
Authors: Sanishvili, R. / Yakunin, A.F. / Laskowski, R.A. / Skarina, T. / Evdokimova, E. / Doherty-Kirby, A. / Lajoie, G.A. / Thornton, J.M. / Arrowsmith, C.H. / Savchenko, A. / Joachimiak, A. / Edwards, A.M.
History
DepositionJun 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BioH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1874
Polymers28,9721
Non-polymers2143
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.210, 75.210, 49.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe monomer in the asymmetric unit is a whole biological unit.

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Components

#1: Protein BioH protein


Mass: 28972.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BioH / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13001
#2: Chemical ChemComp-3OH / 3-HYDROXY-PROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 1.3M tri Na Citrate, 0.1M Tris, 15% ethylene glycol, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.2 Msodium citrate trihydrate1reservoir
20.1 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979464, 0.953732, 1.03321
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 15, 2001
Details: sagitally focusing monochromator, vertically focusing mirror
RadiationMonochromator: Sagitally focusing Si(111) double crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794641
20.9537321
31.033211
ReflectionResolution: 1.63→100 Å / Num. all: 34646 / Num. obs: 33538 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.075 / Net I/σ(I): 16.5
Reflection shellResolution: 1.63→1.69 Å / Mean I/σ(I) obs: 1.2 / Num. unique all: 2828 / Rsym value: 0.595 / % possible all: 82.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 114995 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 82.5 % / Num. unique obs: 3061 / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.1.05refinement
dtDisplaydata collection
HKL-2000data reduction
CNSrefinement
d*TREKdata scaling
d*TREKdata reduction
DTDISPLAYdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→74.54 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.933 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18838 1422 5 %RANDOM
Rwork0.14523 ---
obs0.14735 27141 93.85 %-
all-30435 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.249 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 14 238 2248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212327
X-RAY DIFFRACTIONr_bond_other_d0.0030.022174
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.953158
X-RAY DIFFRACTIONr_angle_other_deg2.32935079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.56515455
X-RAY DIFFRACTIONr_chiral_restr0.1430.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022551
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02468
X-RAY DIFFRACTIONr_nbd_refined0.2860.2539
X-RAY DIFFRACTIONr_nbd_other0.2680.22506
X-RAY DIFFRACTIONr_nbtor_other0.0980.21273
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.218
X-RAY DIFFRACTIONr_mcbond_it1.1071.51373
X-RAY DIFFRACTIONr_mcangle_it1.79122248
X-RAY DIFFRACTIONr_scbond_it2.653954
X-RAY DIFFRACTIONr_scangle_it3.9614.5910
LS refinement shellResolution: 1.7→1.792 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.256 175
Rwork0.212 3631
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)
11.596-0.22170.29922.1184-0.08511.73190.01790.01090.05180.0451-0.03120.0583-0.0046-0.0260.01330.0210.01470.00920.019-0.01110.039318.970710.82314.3217
20.9386-0.4449-0.14381.3232-0.45011.10530.04830.2257-0.0386-0.1064-0.0571-0.31460.05210.38170.00880.13380.0224-0.00630.162-0.00550.140434.47222.570911.6658
31.6269-0.35730.07071.8027-0.15251.40510.02330.01930.09150.0099-0.0147-0.0578-0.05850.0426-0.00860.1710.0069-0.01140.1592-0.01550.140822.40289.339113.223
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1093 - 109
2X-RAY DIFFRACTION1AA188 - 258188 - 258
3X-RAY DIFFRACTION2AA110 - 187110 - 187
4X-RAY DIFFRACTION3AA303 - 5401 - 238
Refinement
*PLUS
Lowest resolution: 75 Å / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_d0.0220.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9051.95
X-RAY DIFFRACTIONr_plane_restr0.0110.02
X-RAY DIFFRACTIONr_chiral_restr0.1310.2
LS refinement shell
*PLUS
Lowest resolution: 1.79 Å / Rfactor Rfree: 0.246

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