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- PDB-3lp5: The crystal structure of the putative cell surface hydrolase from... -

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Basic information

Entry
Database: PDB / ID: 3lp5
TitleThe crystal structure of the putative cell surface hydrolase from Lactobacillus plantarum WCFS1
ComponentsPutative cell surface hydrolase
KeywordsHYDROLASE / surface hydrolase / Lactobacillus plantarum / structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Protein of unknown function DUF915, hydrolase-like / Alpha/beta hydrolase of unknown function (DUF915) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell surface hydrolase, DUF915 family / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Li, H. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the putative cell surface hydrolase from Lactobacillus plantarum WCFS1
Authors: Zhang, R. / Li, H. / Cobb, G. / Joachimiak, A.
History
DepositionFeb 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Putative cell surface hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1653
Polymers28,1191
Non-polymers462
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.680, 122.154, 38.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative cell surface hydrolase


Mass: 28118.846 Da / Num. of mol.: 1 / Fragment: sequence database residues 40-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: GI:28270776, lp_1165 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q88XN2, UniProt: F9UMW5*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M tri-sodium citrate dehydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→61.08 Å / Num. all: 16365 / Num. obs: 16267 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.187 / Net I/σ(I): 15.36
Reflection shellResolution: 2→2.052 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1243 / % possible all: 96.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→61.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.473 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.175
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23647 866 5.1 %RANDOM
Rwork0.17462 ---
obs0.17768 16267 99.4 %-
all-16365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.065 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2--0.05 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2→61.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 2 154 2136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222023
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9442743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22924.28691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69215350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9831510
X-RAY DIFFRACTIONr_chiral_restr0.130.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211518
X-RAY DIFFRACTIONr_mcbond_it1.0811.51245
X-RAY DIFFRACTIONr_mcangle_it1.9722022
X-RAY DIFFRACTIONr_scbond_it3.3283778
X-RAY DIFFRACTIONr_scangle_it5.6494.5721
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 63 -
Rwork0.23 1139 -
obs-1202 96.7 %
Refinement TLS params.Method: refined / Origin x: 13.2067 Å / Origin y: 18.8965 Å / Origin z: 28.2748 Å
111213212223313233
T0.0319 Å20.0026 Å2-0.0106 Å2-0.0394 Å2-0.0074 Å2--0.0121 Å2
L1.3885 °20.0767 °20.0019 °2-0.8423 °2-0.274 °2--0.4476 °2
S0.0222 Å °-0.0365 Å °-0.0764 Å °0.0107 Å °-0.0221 Å °-0.0276 Å °-0.0231 Å °-0.0478 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 200
5X-RAY DIFFRACTION1A201 - 249

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