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- PDB-1idj: PECTIN LYASE A -

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Basic information

Entry
Database: PDB / ID: 1idj
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 / molecular replacement, SIR, INTERCRYSTAL AVERAGING / Resolution: 2.4 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PECTIN LYASE A
B: PECTIN LYASE A


Theoretical massNumber of molelcules
Total (without water)75,9182
Polymers75,9182
Non-polymers00
Water4,630257
1
A: PECTIN LYASE A


Theoretical massNumber of molelcules
Total (without water)37,9591
Polymers37,9591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PECTIN LYASE A


Theoretical massNumber of molelcules
Total (without water)37,9591
Polymers37,9591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.900, 52.400, 76.300
Angle α, β, γ (deg.)78.60, 90.10, 104.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.000987, 8.5E-5), (0.000986, -0.999973, 0.007283), (9.2E-5, -0.007283, -0.999974)
Vector: 10.7262, 99.68973, 109.03496)

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Components

#1: Protein PECTIN LYASE A


Mass: 37959.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SECRETED PROTEIN / Source: (natural) Aspergillus niger (mold) / Strain: N400 / References: UniProt: Q01172, pectin lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGLYCOSYLATION SITES SUGGESTED BY ELECTRON DENSITY: N109, T68 SACCHARIDES ARE NOT INCLUDED IN THE ...GLYCOSYLATION SITES SUGGESTED BY ELECTRON DENSITY: N109, T68 SACCHARIDES ARE NOT INCLUDED IN THE MODEL OR IN THE STATISTICS PRESENTED IN THIS ENTRY.
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: 2.46 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5
Details: 28% PEG 6000, 0.1 M NA-CACODYLATE AT PH 6.5, 0.2 M NA-ACETATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Jenkins, J., (1996) Acta Crystallogr.,Sect.D, 52, 402.
pH: 8.5
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: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Feb 15, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→33.3 Å / Num. obs: 23191 / % possible obs: 84.3 % / Observed criterion σ(I): 3 / Redundancy: 1.9 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.64 Å / Redundancy: 1 % / Mean I/σ(I) obs: 3.6 / % possible all: 48.5
Reflection
*PLUS
Num. measured all: 44141
Reflection shell
*PLUS
% possible obs: 92.2 % / Rmerge(I) obs: 0.125

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Processing

Software
NameVersionClassification
XENGENdata collection
ROTAVATAdata reduction
Agrovatadata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: molecular replacement, SIR, INTERCRYSTAL AVERAGING
Starting model: PARTIALLY REFINED MODEL FROM PECTIN LYASE A P212121 (1IDK)

1idk


Resolution: 2.4→33.3 Å / Cross valid method: FREE R + SECOND CRYSTAL FORM / σ(F): 0
Details: OVERALL ANISOTROPIC SCALING, BULK SOLVENT CORRECTION, RESTRAINED NCS AND RESTRAINED ISOTROPIC INDIVIDUAL TEMPERATURE FACTOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1196 5 %FREERFLAG (CCP4)
Rwork0.16 ---
obs0.16 23191 84.25 %-
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.218 Å20.546 Å20.635 Å2
2---0.136 Å24.453 Å2
3---3.3552 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 0 257 2928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.373
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.33
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.119
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it3.61.5
X-RAY DIFFRACTIONx_scangle_it3.622
Refine LS restraints NCSNCS model details: RESTRICTED NCS / Rms dev Biso : 0.296 Å2 / Rms dev position: 0.0087 Å / Weight Biso : 0.2 / Weight position: 500
LS refinement shellResolution: 2.4→2.64 Å
RfactorNum. reflection% reflection
Rfree0.294 173 2.5 %
Rwork0.267 3173 -
obs--48.5 %
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
Refinement
*PLUS
Rfactor obs: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.33
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.119

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