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- PDB-3vmv: Crystal structure of pectate lyase Bsp165PelA from Bacillus sp. N165 -

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Basic information

Entry
Database: PDB / ID: 3vmv
TitleCrystal structure of pectate lyase Bsp165PelA from Bacillus sp. N165
ComponentsPectate lyase
KeywordsLYASE / Polysaccharide Lyase Family 1 / beta-helix / pectolytic / polygalacturonate
Function / homology
Function and homology information


pectate lyase activity / polysaccharide catabolic process / extracellular region
Similarity search - Function
Pectate lyase / Pectin lyase family / Pectate lyase / Amb_all / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus (Bacillus rRNA group 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsZheng, Y. / Huang, C.H. / Liu, W. / Ko, T.P. / Xue, Y. / Zhou, C. / Zhang, G. / Guo, R.T. / Ma, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structure and substrate-binding mode of a novel pectate lyase from alkaliphilic Bacillus sp. N16-5.
Authors: Zheng, Y. / Huang, C.H. / Liu, W. / Ko, T.P. / Xue, Y. / Zhou, C. / Guo, R.T. / Ma, Y.
History
DepositionDec 16, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1713
Polymers35,9791
Non-polymers1922
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.874, 48.473, 52.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-822-

HOH

21A-826-

HOH

31A-849-

HOH

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Components

#1: Protein Pectate lyase


Mass: 35979.137 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP RESIDUES 37-362)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Strain: N16-5 / Gene: GU088530, pelA / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D0VP31, pectate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 48.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.18M Li2SO4, 0.085M Tris-HCl, pH 8.5, 24% PEG 4000, 15% v/v Glycerol anhydrous, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→25 Å / Num. obs: 51969 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.301 / Num. unique all: 38662 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QXZ

2qxz


Resolution: 1.54→24.639 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 16.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 2648 5.11 %RANDOM
Rwork0.166 ---
obs0.1673 51866 99.22 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.774 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3481 Å20 Å2-0 Å2
2--1.1167 Å20 Å2
3----5.4647 Å2
Refinement stepCycle: LAST / Resolution: 1.54→24.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 10 349 2887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142600
X-RAY DIFFRACTIONf_angle_d1.5393540
X-RAY DIFFRACTIONf_dihedral_angle_d13.338915
X-RAY DIFFRACTIONf_chiral_restr0.112371
X-RAY DIFFRACTIONf_plane_restr0.009475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.54-1.5680.21231340.1702252898
1.568-1.59820.19791210.16862588100
1.5982-1.63080.22571450.16552563100
1.6308-1.66620.18241390.16372595100
1.6662-1.7050.20151390.1512544100
1.705-1.74760.19471310.15072595100
1.7476-1.79480.17981460.15052583100
1.7948-1.84760.1811380.14572557100
1.8476-1.90720.16271480.14322593100
1.9072-1.97540.15711470.13712553100
1.9754-2.05440.16491370.1412604100
2.0544-2.14790.18581480.14942570100
2.1479-2.26110.16811270.14812618100
2.2611-2.40260.18421420.15052624100
2.4026-2.58790.17921440.16252607100
2.5879-2.8480.21961560.1739258499
2.848-3.25930.19371210.1783259497
3.2593-4.10330.1831390.1709255796
4.1033-24.64260.22671460.204276198
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)
10.6110.2141-0.07940.4853-0.16110.8328-0.0260.0424-0.0261-0.0062-0.01130.0032-0.03990.0315-0.04240.0629-0.0155-0.00840.06290.00510.0753-17.733716.369114.9827
20.35720.12610.00530.18920.01640.2218-0.04920.0347-0.00090.00650.00410.0248-0.0403-0.0095-0.00610.1272-0.00770.00080.09920.00410.1133-16.961817.105314.8415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:326)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 501:849)

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