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- PDB-1bn8: BACILLUS SUBTILIS PECTATE LYASE -

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Basic information

Entry
Database: PDB / ID: 1bn8
TitleBACILLUS SUBTILIS PECTATE LYASE
ComponentsPROTEIN (PECTATE LYASE)
KeywordsLYASE / PARALLEL BETA-HELIX
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding
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 subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsPickersgill, R. / Harris, G. / Jenkins, J.
CitationJournal: Nat.Struct.Biol. / Year: 1994
Title: The structure of Bacillus subtilis pectate lyase in complex with calcium.
Authors: Pickersgill, R. / Jenkins, J. / Harris, G. / Nasser, W. / Robert-Baudouy, J.
History
DepositionJul 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 5, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: PROTEIN (PECTATE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5882
Polymers45,5481
Non-polymers401
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.900, 89.000, 50.700
Angle α, β, γ (deg.)90.00, 108.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (PECTATE LYASE) / EC 4.2.2.2


Mass: 45547.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / Strain: S1103 / References: UniProt: P39116, pectate lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.7 Å3/Da / Density % sol: 53.02 %
Crystal growpH: 6.5
Details: TYPE II CRYSTALS: 35 - 45 % 2-METHYL-2,4-PENTANDIOL 50 MM MOPS / 50 MM ETHANOLAMINE PH IN THE RANGE 6.50 TO 8.75
PH range: 6.50-8.75
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Jenkins, J.A., (1992) J. Mol. Biol., 228, 1255. / PH range low: 6.5 / PH range high: 6.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135-40 %MPD1reservoir
250 mMMOPS1reservoir
350 mMethanolamine1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 187670 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.179 --
obs-43201 99 %
Displacement parametersBiso mean: 13.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 1 209 3276
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0050.02
X-RAY DIFFRACTIONp_angle_d0.0190.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0160.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6762
X-RAY DIFFRACTIONp_mcangle_it1.1583
X-RAY DIFFRACTIONp_scbond_it0.9642
X-RAY DIFFRACTIONp_scangle_it1.5433
X-RAY DIFFRACTIONp_plane_restr0.0170.03
X-RAY DIFFRACTIONp_chiral_restr0.0780.03
X-RAY DIFFRACTIONp_singtor_nbd0.1720.3
X-RAY DIFFRACTIONp_multtor_nbd0.2310.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.0970.3
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor12.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3120
X-RAY DIFFRACTIONp_special_tor

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