+Open data
-Basic information
Entry | Database: PDB / ID: 1qml | ||||||
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Title | Hg complex of yeast 5-aminolaevulinic acid dehydratase | ||||||
Components | 5-AMINOLAEVULINIC ACID DEHYDRATASE | ||||||
Keywords | DEHYDRATASE / ALDOLASE / TIM BARREL / TETRAPYRROLE SYNTHESIS | ||||||
Function / homology | Function and homology information Heme biosynthesis / porphobilinogen synthase / porphobilinogen synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / Neutrophil degranulation / zinc ion binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Erskine, P.T. / Senior, N. / Warren, M.J. / Wood, S.P. / Cooper, J.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: MAD Analyses of Yeast 5-Aminolaevulinic Acid Dehydratase. Their Use in Structure Determination and in Defining the Metal Binding Sites Authors: Erskine, P.T. / Duke, E.M.H. / Tickle, I.J. / Senior, N.M. / Warren, M.J. / Cooper, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qml.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qml.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qml_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 1qml_full_validation.pdf.gz | 461 KB | Display | |
Data in XML | 1qml_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1qml_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/1qml ftp://data.pdbj.org/pub/pdb/validation_reports/qm/1qml | HTTPS FTP |
-Related structure data
Related structure data | 1qnvC 1aw5S 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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Unit cell |
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-Components
#1: Protein | Mass: 37785.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HG CHLORIDE CO-CRYSTAL / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Plasmid: PNS1 / Strain: NS1(JM109/PNS1) / References: UniProt: P05373, porphobilinogen synthase |
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#2: Chemical | ChemComp-HG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 59 % |
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Crystal grow | pH: 8 / Details: AS FOR 1AW5 WITH 1MM HGCL, pH 8.00 |
Crystal grow | *PLUS Method: vapor diffusion, hanging drop |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.875 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.875 Å / Relative weight: 1 |
Reflection | Resolution: 3→14.6 Å / Num. obs: 9264 / % possible obs: 99 % / Redundancy: 7.5 % / Biso Wilson estimate: 66.6 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.7 / % possible all: 99.4 |
Reflection shell | *PLUS % possible obs: 99.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AW5 Resolution: 3→14.5 Å / Cross valid method: FREE R-VALUE / σ(F): 3
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Displacement parameters | Biso mean: 29.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 14.5 Å / Luzzati sigma a obs: 0.5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→14.5 Å
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Refine LS restraints |
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