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- PDB-3bjr: Crystal structure of a putative carboxylesterase (lp_1002) from l... -

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Basic information

Entry
Database: PDB / ID: 3bjr
TitleCrystal structure of a putative carboxylesterase (lp_1002) from lactobacillus plantarum wcfs1 at 2.09 A resolution
ComponentsPutative carboxylesterase
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / BD-FAE / : / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipase/esterase / :
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative carboxylesterase (NP_784706.1) from Lactobacillus plantarum at 2.09 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3542
Polymers31,2621
Non-polymers921
Water2,576143
1
A: Putative carboxylesterase
hetero molecules

A: Putative carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7074
Polymers62,5232
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.620, 93.620, 99.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative carboxylesterase


Mass: 31261.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Species: Lactobacillus plantarum / Strain: WCFS1 / NCIMB 8826 / Gene: NP_784706.1, lp_1002 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q88Y04, UniProt: F9UMI7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.03 Å3/Da / Density % sol: 69.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 0.8M (NH4)2SO4, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97939, 0.97953
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979391
30.979531
ReflectionResolution: 2.09→29.285 Å / Num. obs: 29521 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.93 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.09-2.160.612.2161874554183.2
2.16-2.250.5122.8229985888197.8
2.25-2.350.4223.3218615597198.2
2.35-2.480.3294.1233005953197.9
2.48-2.630.2455.3214075471197.7
2.63-2.830.1697.3219765638198.6
2.83-3.120.1169.7227955864198.5
3.12-3.570.07913.8219735702198.9
3.57-4.490.05918.1216375741199.2
4.49-29.2850.04220.5221225795198.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.09→29.285 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.957 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.112
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GLYCEROL MOLECULE FROM CRYOPROTECTANT IS MODELED IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1494 5.1 %RANDOM
Rwork0.175 ---
obs0.176 29517 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.806 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å21.02 Å20 Å2
2--2.05 Å20 Å2
3----3.07 Å2
Refinement stepCycle: LAST / Resolution: 2.09→29.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 6 143 2012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221970
X-RAY DIFFRACTIONr_bond_other_d0.0020.021223
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9422718
X-RAY DIFFRACTIONr_angle_other_deg1.09533010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3975250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93124.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66215271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.156155
X-RAY DIFFRACTIONr_chiral_restr0.0950.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022220
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02378
X-RAY DIFFRACTIONr_nbd_refined0.2070.3402
X-RAY DIFFRACTIONr_nbd_other0.1830.31250
X-RAY DIFFRACTIONr_nbtor_refined0.1820.5961
X-RAY DIFFRACTIONr_nbtor_other0.0910.5919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.5184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.316
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.515
X-RAY DIFFRACTIONr_mcbond_it2.04731296
X-RAY DIFFRACTIONr_mcbond_other0.5173494
X-RAY DIFFRACTIONr_mcangle_it3.17752017
X-RAY DIFFRACTIONr_scbond_it5.0498807
X-RAY DIFFRACTIONr_scangle_it6.19111701
LS refinement shellResolution: 2.09→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 105 -
Rwork0.272 1806 -
all-1911 -
obs--86.9 %
Refinement TLS params.Method: refined / Origin x: 9.242 Å / Origin y: 50.235 Å / Origin z: 7.348 Å
111213212223313233
T-0.1212 Å20.0204 Å2-0.0012 Å2--0.0824 Å2-0.0136 Å2---0.1255 Å2
L2.0977 °2-0.686 °2-0.759 °2-1.2413 °20.0769 °2--3.6581 °2
S0.067 Å °-0.0265 Å °0.0592 Å °0.0401 Å °-0.04 Å °-0.0029 Å °-0.2156 Å °-0.1226 Å °-0.0269 Å °

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