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- PDB-3bxp: CRYSTAL STRUCTURE OF A PUTATIVE CARBOXYLESTERASE (LP_2923) FROM L... -

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Basic information

Entry
Database: PDB / ID: 3bxp
TitleCRYSTAL STRUCTURE OF A PUTATIVE CARBOXYLESTERASE (LP_2923) FROM LACTOBACILLUS PLANTARUM WCFS1 AT 1.70 A RESOLUTION
ComponentsPutative lipase/esterase
KeywordsHYDROLASE / PUTATIVE CARBOXYLESTERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


hydrolase activity / metal ion binding / identical protein binding
Similarity search - Function
: / 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
S-1,2-PROPANEDIOL / R-1,2-PROPANEDIOL / Lipase/esterase / :
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative carboxylesterase (NP_786266.1) from Lactobacillus plantarum at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: 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 1.4Feb 1, 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 30, 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. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative lipase/esterase
B: Putative lipase/esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,61412
Polymers61,5702
Non-polymers1,04510
Water6,900383
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.595, 94.222, 58.758
Angle α, β, γ (deg.)90.000, 107.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative lipase/esterase


Mass: 30784.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Species: Lactobacillus plantarum / Strain: WCFS1 / NCIMB 8826 / Gene: NP_786266.1, lp_2923 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q88TL9, UniProt: F9US10*PLUS

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Non-polymers , 5 types, 393 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 30.0% 1,2-propanediol, 20.0% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97901 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 1.7→28.433 Å / Num. obs: 59209 / % possible obs: 96.8 % / Redundancy: 5 % / Biso Wilson estimate: 23.465 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.743.80.5321.51454138370.53286.4
1.74-1.793.90.4291.81662342580.42996.5
1.79-1.843.90.3382.31610841190.33896.4
1.84-1.93.90.272.91574340300.2796.9
1.9-1.963.90.1953.91522239000.19596.7
1.96-2.033.90.15151470137600.15197.3
2.03-2.113.90.1295.71429136640.12997.2
2.11-2.193.90.1086.31373035180.10897.5
2.19-2.293.90.0966.81327533990.09697.6
2.29-2.44.70.1016.61529232550.10197.8
2.4-2.535.10.0927.21594531020.09298
2.53-2.695.80.0867.71703629590.08698.1
2.69-2.876.80.0788.51856627410.07898.4
2.87-3.17.70.0748.42006026050.07498.9
3.1-3.47.70.0659.31832023830.06598.6
3.4-3.87.60.0619.51647121620.06199
3.8-4.397.50.05810.11435819060.05899.1
4.39-5.387.50.05210.71229416480.05299.2
5.38-7.67.30.05411.2926312690.05499.7
7.6-28.43370.04713.148726940.04797.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→28.433 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.975 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.098
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. CHLORIDE ION, HEPES AND 1,2-PROPANEDIOL MOLECULES FROM CRYSTALLIZATION ARE MODELED IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2995 5.1 %RANDOM
Rwork0.166 ---
obs0.168 59208 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.685 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-1.04 Å2
2---0.74 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 66 383 4429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214298
X-RAY DIFFRACTIONr_bond_other_d0.0010.022733
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9295899
X-RAY DIFFRACTIONr_angle_other_deg1.07936676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96623.88183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92615612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1191519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214877
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02876
X-RAY DIFFRACTIONr_mcbond_it1.91732681
X-RAY DIFFRACTIONr_mcbond_other0.58731081
X-RAY DIFFRACTIONr_mcangle_it2.76654324
X-RAY DIFFRACTIONr_scbond_it4.12981617
X-RAY DIFFRACTIONr_scangle_it5.611111575
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 199 -
Rwork0.211 3704 -
all-3903 -
obs--86.89 %
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)
10.52540.04810.15170.675-0.01030.36160.007-0.037-0.01930.003-0.01060.0644-0.0487-0.02110.0035-0.0215-0.01110.0063-0.0208-0.0085-0.0313-2.931331.546344.6912
20.2831-0.09720.03450.7687-0.07310.86060.00310.0132-0.02360.0258-0.00860.03980.0156-0.04740.0055-0.047-0.00770.0024-0.0244-0.0118-0.0203-21.138148.23416.4949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 2731 - 274
2X-RAY DIFFRACTION2BB0 - 2731 - 274

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