+Open data
-Basic information
Entry | Database: PDB / ID: 1idj | ||||||
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Title | PECTIN LYASE A | ||||||
Components | PECTIN LYASE A | ||||||
Keywords | LYASE / 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 | ||||||
Biological species | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / molecular replacement, SIR, INTERCRYSTAL AVERAGING / Resolution: 2.4 Å | ||||||
Authors | Mayans, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1idj.cif.gz | 140.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1idj.ent.gz | 114.8 KB | Display | PDB format |
PDBx/mmJSON format | 1idj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1idj_validation.pdf.gz | 434.2 KB | Display | wwPDB validaton report |
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Full document | 1idj_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 1idj_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 1idj_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1idj ftp://data.pdbj.org/pub/pdb/validation_reports/id/1idj | HTTPS FTP |
-Related structure data
Related structure data | 1idkSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, 0.000987, 8.5E-5), Vector: |
-Components
#1: Protein | 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 / | Compound details | GLYCOSYLATION SITES SUGGESTED BY ELECTRON DENSITY: N109, T68 SACCHARIDES ARE NOT INCLUDED IN THE ...GLYCOSYLAT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 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 dropDetails: Jenkins, J., (1996) Acta Crystallogr.,Sect.D, 52, 402. pH: 8.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Feb 15, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement, SIR, INTERCRYSTAL AVERAGING Starting model: PARTIALLY REFINED MODEL FROM PECTIN LYASE A P212121 (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
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Displacement parameters | Biso mean: 37.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→33.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS 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 shell | Resolution: 2.4→2.64 Å
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Xplor file |
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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
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