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- PDB-1idk: PECTIN LYASE A -

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Basic information

Entry
Database: PDB / ID: 1idk
TitlePECTIN LYASE A
ComponentsPECTIN LYASE A
KeywordsLYASE / GLYCOPROTEIN / MULTIGENE FAMILY
Function / homology
Function and homology information


pectin lyase / pectin lyase activity / pectate lyase activity / polysaccharide catabolic process / cell wall organization / 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 speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, MIR / Resolution: 1.93 Å
AuthorsMayans, O. / Scott, M. / Connerton, I. / Gravesen, T. / Benen, J. / Visser, J. / Pickersgill, R. / Jenkins, J.
Citation
Journal: Structure / Year: 1997
Title: Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases.
Authors: Mayans, O. / Scott, M. / Connerton, I. / Gravesen, T. / Benen, J. / Visser, J. / Pickersgill, R. / Jenkins, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary X-Ray Analysis of Pectin Lyase a from Aspergillus Niger
Authors: Jenkins, J. / Scott, M. / Mayans, O. / Pickersgill, R. / Harris, G. / Connerton, I. / Gravesen, T.
#2: Journal: 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
DepositionOct 4, 1996Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PECTIN LYASE A


Theoretical massNumber of molelcules
Total (without water)37,9821
Polymers37,9821
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.400, 83.500, 93.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PECTIN LYASE A


Mass: 37982.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SECRETED PROTEIN / Source: (natural) Aspergillus niger (mold) / Strain: 4M-147 / References: UniProt: Q01172, pectin lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 8.5
Details: 28% PEG 4000, 100 MM SODIUM ACETATE, 100 MM TRIS-HCL AT PH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Jenkins, J., (1996) Acta Crystallogr.,Sect.D, 52, 402.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120.4 mg/mlprotein1drop
29.3 %PEG40001drop
333 mMsodium acetate1drop
428 %PEG40001reservoir
5100 mMsodium acetate1reservoir

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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: Jun 9, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.93→25.44 Å / Num. obs: 25695 / % possible obs: 94 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.66 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.47
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.3 / % possible all: 72.3
Reflection
*PLUS
Num. measured all: 80561
Reflection shell
*PLUS
% possible obs: 84.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovata(CCP4 2.13)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4V. 2.13 (AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: molecular replacement, MIR
Starting model: DERIVED FROM BACILLUS SUBTILIS PECTATE LYASE

Resolution: 1.93→15 Å / Cross valid method: FREE R + R VALUE OF SECOND CRYSTAL FORM / σ(F): 2
Details: OVERALL ANISOTROPIC SCALING, BULK SOLVENT CORRECTION AND RESTRAINED ISOTROPIC INDIVIDUAL TEMPERATURE FACTOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1122 5 %FREERFLAG (CCP4 2.15)
Rwork0.188 ---
obs0.188 23147 84.5 %-
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--12.8 Å20 Å20 Å2
2--7.01 Å20 Å2
3---5.78 Å2
Refinement stepCycle: LAST / Resolution: 1.93→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 0 175 2850
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.382
X-RAY DIFFRACTIONx_scangle_it1.662.5
LS refinement shellResolution: 1.93→1.97 Å
RfactorNum. reflection% reflection
Rfree0.268 53 2.97 %
Rwork0.286 1101 -
obs--61.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.22

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