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- PDB-2bsp: BACILLUS SUBTILIS PECTATE LYASE R279K MUTANT -

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Basic information

Entry
Database: PDB / ID: 2bsp
TitleBACILLUS SUBTILIS PECTATE LYASE R279K MUTANT
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
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 subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPickersgill, R.
CitationJournal: To be Published
Title: The Conserved Arginine Proximal to the Essential Calcium of Bacillus Subtilis Pectate Lyase Stabilizes the Transition State
Authors: Pickersgill, R. / Worboys, K. / Scott, M. / Cummings, N. / Cooper, A. / Jenkins, J. / Smith, D.
History
DepositionJul 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PECTATE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5602
Polymers45,5201
Non-polymers401
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.430, 69.710, 60.230
Angle α, β, γ (deg.)90.00, 112.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (PECTATE LYASE)


Mass: 45519.773 Da / Num. of mol.: 1 / Mutation: R279K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: S1103 / Plasmid: PLYSS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / 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.: 246 / 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: 2.19 Å3/Da / Density % sol: 38 %
Crystal growpH: 4.6
Details: 30 % PEG 4000 0.2 M AMMONIUM SULPHATE 0.1 M SODIUM ACETATE AT PH 4.6

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→56 Å / Num. obs: 35454 / % possible obs: 96 % / Observed criterion σ(I): 1.8 / Redundancy: 2.6 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 4 / % possible all: 99

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Processing

Software
NameVersionClassification
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE STRUCTURE

Resolution: 1.8→10 Å / SU B: 1.33 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.14 / Details: X-PLOR USED PRIOR TO REFMAC
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3471 10 %RANDOM
Rwork0.196 ---
obs-31507 96 %-
Displacement parametersBiso mean: 11.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 1 246 3310
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0050.02
X-RAY DIFFRACTIONp_angle_d0.020.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0180.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7222
X-RAY DIFFRACTIONp_mcangle_it1.2043
X-RAY DIFFRACTIONp_scbond_it0.9772
X-RAY DIFFRACTIONp_scangle_it1.553
X-RAY DIFFRACTIONp_plane_restr0.0170.03
X-RAY DIFFRACTIONp_chiral_restr0.080.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1030.3
X-RAY DIFFRACTIONp_planar_tor3.47
X-RAY DIFFRACTIONp_staggered_tor15.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.520
X-RAY DIFFRACTIONp_special_tor

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