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- PDB-3vmw: Crystal structure of pectate lyase Bsp165PelA from Bacillus sp. N... -

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Basic information

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


pectate lyase activity / polysaccharide catabolic process / extracellular region
Similarity search - Function
Pectin lyase family / Pectate lyase / 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: 1.9 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 17, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0067
Polymers35,9791
Non-polymers1,0276
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.902, 48.174, 52.470
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 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: Polysaccharide alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpAa1-4DGalpAa1-4DGalpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2112A-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
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: 1.9→25 Å / Num. obs: 28061 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.223 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VMV

3vmv


Resolution: 1.9→24.52 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 1408 5.03 %RANDOM
Rwork0.1544 ---
obs0.1568 27967 98.56 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.739 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8144 Å20 Å2-0 Å2
2--7.1434 Å20 Å2
3----5.3291 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 61 184 2773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142650
X-RAY DIFFRACTIONf_angle_d1.4423615
X-RAY DIFFRACTIONf_dihedral_angle_d26.838992
X-RAY DIFFRACTIONf_chiral_restr0.122385
X-RAY DIFFRACTIONf_plane_restr0.006478
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9001-1.96790.26891370.1775249695
1.9679-2.04670.20831230.1508255096
2.0467-2.13980.24021480.1379259398
2.1398-2.25250.20961250.1402265599
2.2525-2.39360.20861390.1352684100
2.3936-2.57820.23951410.14732638100
2.5782-2.83730.19571630.15242686100
2.8373-3.24710.1941510.15392688100
3.2471-4.08790.18661420.14742729100
4.0879-24.52210.19741390.1745284098
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)
11.9163-0.770.46270.9422-0.38561.1443-0.0201-0.20630.0253-0.02450.0396-0.0139-0.01060.003900.11890.00620.00730.1207-0.00440.1356-18.02456.9983-15.2649
20.5278-0.48480.12170.4457-0.08450.2804-0.0558-0.11430.0362-0.06030.0657-0.0838-0.06770.0314-00.17160.0034-0.00320.1820.00810.1687-16.72896.5779-15.3711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:326)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 1001:1184)

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