+Open data
-Basic information
Entry | Database: PDB / ID: 1w7c | |||||||||
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Title | PPLO at 1.23 Angstroms | |||||||||
Components | LYSYL OXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / AMINE OXIDASE / QUINOPROTEIN / TOPAQUINONE ENZYME | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor / diamine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | PICHIA PASTORIS (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å | |||||||||
Authors | Duff, A.P. / Cohen, A.E. / Ellis, P.J. / Guss, J.M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: The 1.23 A Structure of Pichia Pastoris Lysyl Oxidase Reveals a Lysine-Lysine Cross-Link Authors: Duff, A.P. / Cohen, A.E. / Ellis, P.J. / Hilmer, K. / Langley, D.B. / Dooley, D.M. / Freeman, H.C. / Guss, J.M. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w7c.cif.gz | 491.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w7c.ent.gz | 404.8 KB | Display | PDB format |
PDBx/mmJSON format | 1w7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w7c_validation.pdf.gz | 785.7 KB | Display | wwPDB validaton report |
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Full document | 1w7c_full_validation.pdf.gz | 789 KB | Display | |
Data in XML | 1w7c_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 1w7c_validation.cif.gz | 63.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/1w7c ftp://data.pdbj.org/pub/pdb/validation_reports/w7/1w7c | HTTPS FTP |
-Related structure data
Related structure data | 1n9eS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 85289.125 Da / Num. of mol.: 1 / Fragment: PPLO HOMOLENZYME HALF DIMER, RESIDUES 41-787 Source method: isolated from a genetically manipulated source Details: RESIDUE A478 AN ACTIVE SITE TYR RESIDUE, WAS AUTOCATALYTICALLY MODIFIED TO TPQ. THE ENZYME IS GLYCOSYLATED AT ASN A81, ASN A104, ASN A191, ASN A309, AND ASN A 434. RESIDUE LYS 66 IS ...Details: RESIDUE A478 AN ACTIVE SITE TYR RESIDUE, WAS AUTOCATALYTICALLY MODIFIED TO TPQ. THE ENZYME IS GLYCOSYLATED AT ASN A81, ASN A104, ASN A191, ASN A309, AND ASN A 434. RESIDUE LYS 66 IS PARTIALLY CROSS-LINKED WITH RESIDUE LYS 778 TO FORM DEHYDROLYSINONORLEUCINE Source: (gene. exp.) PICHIA PASTORIS (fungus) Description: ISOLATION EXUDATE OF OAK, FRANCE HISTORY, ATCC, CBS, A.GUILLIERMOND Cell line (production host): GS115 / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q96X16, protein-lysine 6-oxidase |
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-Sugars , 2 types, 5 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#8: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 1060 molecules
#3: Chemical | ChemComp-CU / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-IMD / | #9: Water | ChemComp-HOH / | |
-Details
Compound details | CATALYTIC ACTIVITY: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 THE TPQ SIDE CHAIN IS POORLY RESOLVED, ...CATALYTIC ACTIVITY: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 THE TPQ SIDE CHAIN IS POORLY RESOLVED, BUT IS DEFINATELY |
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Sequence details | RESIDUES 1-40 ARE CLEAVED, AS CONFIRMED BY N-TERMINAL PROTEIN SEQUENCING. NINE SEQUENCE CONFLICTS ...RESIDUES 1-40 ARE CLEAVED, AS CONFIRMED BY N-TERMINAL PROTEIN SEQUENCING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.18 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 35% MPD, IMIDAZOLE PH 8.0, 200 MILLIMOLAR MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979805 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 1, 2003 / Details: DOUBLE CRYSTAL MONOCHROMATOR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979805 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→24 Å / Num. obs: 272737 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 2.78 % / Biso Wilson estimate: 14.06 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.77 |
Reflection shell | Resolution: 1.23→1.27 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.394 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N9E Resolution: 1.23→24.01 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.674 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COORDINATES FOR THE UNOBSERVED TPQ 478 SIDE CHAIN HAVE BEEN MODELLED, WITH ZERO OCCUPANCY, IN THE STANDARD ON-COPPER CONFORMATION AS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COORDINATES FOR THE UNOBSERVED TPQ 478 SIDE CHAIN HAVE BEEN MODELLED, WITH ZERO OCCUPANCY, IN THE STANDARD ON-COPPER CONFORMATION AS ALTERNATE CONFORMER A AND IN THE STANDARD OFF-COPPER CONFORMATION AS ALTERNATE CONFORMATION B. THE B-FACTORS ARE SET TO 50.00, BECAUSE THE APPARENTLY REFINED VALUES WERE INAPPROPRIATE. THE COORDINATES HAVE BEEN CAREFULLY MODELLED. THEY ARE REFINED IN TERMS OF STEREOCHEMISTRY BUT NOT USING X-RAY DATA. THEY ARE DESCRIBED AND ILLUSTRATED IN THE PAPER UNDER REVIEW. THE AUTHORS BELIEVE THAT IN THIS CASE THESE COORDINATES SHOULD APPEAR AS ABOVE INTERMIXED WITH THE REFINED COORDINATES. THEIR ABSENCE IS LIKELY TO BE MORE LIABLE TO CONFUSE THAN THEIR PRESENCE, ESPECIALLY WHEN CONSIDERED ALONGSIDE THE PUBLICATION.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.23→24.01 Å
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Refine LS restraints |
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