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- PDB-3d7r: Crystal structure of a putative esterase from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 3d7r
TitleCrystal structure of a putative esterase from Staphylococcus aureus
ComponentsEsterase
KeywordsHYDROLASE / ESTERASE-LIKE / ALPHA/BETA FOLD
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / BROMIDE ION / :
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus USA300_TCH1516 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsLam, R. / Battaile, K.P. / Chan, T. / Romanov, V. / Lam, K. / Soloveychik, M. / Wu-Brown, J. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal structure of a putative esterase from Staphylococcus aureus
Authors: Battaile, K.P. / Lam, R. / Chan, T. / Romanov, V. / Lam, K. / Soloveychik, M. / Wu-Brown, J. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionMay 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,95332
Polymers76,7462
Non-polymers2,20830
Water5,044280
1
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,47716
Polymers38,3731
Non-polymers1,10415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,47716
Polymers38,3731
Non-polymers1,10415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.888, 46.412, 91.688
Angle α, β, γ (deg.)80.820, 89.970, 69.510
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Esterase


Mass: 38372.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300_TCH1516 (bacteria)
Gene: USA300HOU_2331 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIPL
References: UniProt: A8Z540, Hydrolases; Acting on ester bonds

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Non-polymers , 6 types, 310 molecules

#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 42.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG3350, 0.1M NaBr, 15mM Hexamine Cobalt(III) Chloride, cryo-protected using 30% DMSO, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 2, 2007
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 41127 / % possible obs: 97.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.061 / Χ2: 1.025 / Net I/σ(I): 22.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.01-2.083.90.09338121.089191.1
2.08-2.1740.0840470.981197.1
2.17-2.2640.08241671.037197.3
2.26-2.3840.07241021.044197.7
2.38-2.5340.0741560.984197.9
2.53-2.7340.06741491.029198.1
2.73-340.06341651.01198.5
3-3.4440.05941610.983198.7
3.44-4.333.90.0541601.051198.9
4.33-503.90.05442081.047199.1

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.0141.54411160
ANO_10.7702.0141.54404520
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_18.81-41.54004870
ISO_16.3-8.81008720
ISO_15.16-6.30010960
ISO_14.48-5.160013570
ISO_14.01-4.480014860
ISO_13.66-4.010016460
ISO_13.39-3.660017890
ISO_13.18-3.390018850
ISO_13-3.180020470
ISO_12.84-30021680
ISO_12.71-2.840022530
ISO_12.6-2.710023270
ISO_12.49-2.60024840
ISO_12.4-2.490025140
ISO_12.32-2.40026250
ISO_12.25-2.320027610
ISO_12.18-2.250027580
ISO_12.12-2.180029060
ISO_12.06-2.120029560
ISO_12.01-2.060026990
ANO_18.81-41.540.71104360
ANO_16.3-8.810.70408380
ANO_15.16-6.30.744010640
ANO_14.48-5.160.867013190
ANO_14.01-4.480.826014560
ANO_13.66-4.010.802016170
ANO_13.39-3.660.826017560
ANO_13.18-3.390.802018610
ANO_13-3.180.744020250
ANO_12.84-30.746021500
ANO_12.71-2.840.732022330
ANO_12.6-2.710.744022970
ANO_12.49-2.60.726024580
ANO_12.4-2.490.737024950
ANO_12.32-2.40.7026030
ANO_12.25-2.320.768027400
ANO_12.18-2.250.805027270
ANO_12.12-2.180.742028860
ANO_12.06-2.120.794029090
ANO_12.01-2.060.794025820
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 41114
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.66-100670.752514
6.78-8.6661.10.907563
5.76-6.7858.80.894690
5.09-5.7660.80.914802
4.62-5.0961.20.933880
4.25-4.6262.40.936975
3.96-4.2560.10.931078
3.72-3.9660.80.9291127
3.52-3.7260.40.9311151
3.35-3.5262.30.9191250
3.21-3.3563.30.9091334
3.08-3.2159.60.91363
2.96-3.0860.60.9021398
2.86-2.9659.60.9021494
2.76-2.86610.91515
2.68-2.7659.60.8971562
2.6-2.6859.30.9041594
2.53-2.659.50.91700
2.47-2.5358.70.8871667
2.4-2.4759.40.8951747
2.35-2.459.50.8921791
2.3-2.3558.80.8951822
2.25-2.360.80.8821886
2.2-2.2560.40.8751852
2.16-2.259.70.8782011
2.12-2.1660.30.8591945
2.08-2.1261.50.8342013
2.01-2.0865.10.7833390

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.005data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.01→41.56 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.189 / SU B: 6.333 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2083 5.1 %RANDOM
Rwork0.158 ---
obs0.16 41116 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.453 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.01→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 110 280 5221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225039
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9716792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33624.776245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70115898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6431522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023766
X-RAY DIFFRACTIONr_nbd_refined0.2080.22365
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2322
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.221
X-RAY DIFFRACTIONr_mcbond_it0.5671.52985
X-RAY DIFFRACTIONr_mcangle_it1.1424874
X-RAY DIFFRACTIONr_scbond_it2.2932098
X-RAY DIFFRACTIONr_scangle_it3.7024.51916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.0650.2061340.1472565305988.231
2.065-2.1210.2191630.1542793305096.918
2.121-2.1830.1841520.1512754298497.386
2.183-2.250.1991100.1552648283797.215
2.25-2.3230.1921600.152602283697.391
2.323-2.4050.1951390.1542485268597.728
2.405-2.4950.2071280.162386256498.05
2.495-2.5960.1821040.1642380253597.988
2.596-2.7110.1881240.162203236898.269
2.711-2.8430.211920.1642161229498.213
2.843-2.9960.1961080.1642060220298.456
2.996-3.1770.2131040.1661943207498.698
3.177-3.3950.1831060.1561779190998.743
3.395-3.6650.1761010.1461688181198.785
3.665-4.0110.161900.1481556166299.037
4.011-4.480.177780.1531408150099.067
4.48-5.1630.174680.1561289136799.268
5.163-6.2990.236490.1921047110199.546
6.299-8.8070.232400.18583287699.543
8.807-41.5590.206330.16545450496.627
Refinement TLS params.

S32: -0.0042 Å ° / 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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35770.09320.00680.36620.20920.37650.00590.0307-0.00620.02420.0031-0.0046-0.0019-0.009-0.0170.00470.0009-0.0260.0003-0.013639.03912.3333.446
20.42390.062-0.12140.3221-0.11710.42590.00820.02920.0170.03010.00450.0005-0.0062-0.0126-0.02160.0026-0.0012-0.02120.0044-0.016665.15420.8548.556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 30429 - 324
2X-RAY DIFFRACTION2BB9 - 30329 - 323

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