+Open data
-Basic information
Entry | Database: PDB / ID: 1hq6 | |||||||||
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Title | STRUCTURE OF PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE AT PH 8 | |||||||||
Components | (HISTIDINE DECARBOXYLASE) x 2 | |||||||||
Keywords | LYASE / HELIX DISORDER / PH REGULATION / LESS ACTIVE FORM / PYRUVOYL / CARBOXY-LYASE | |||||||||
Function / homology | Function and homology information histidine decarboxylase / histidine decarboxylase activity / L-histidine metabolic process / amino acid metabolic process Similarity search - Function | |||||||||
Biological species | Lactobacillus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Schelp, E. / Worley, S. / Monzingo, A.F. / Ernst, S. / Robertus, J.D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: pH-induced structural changes regulate histidine decarboxylase activity in Lactobacillus 30a. Authors: Schelp, E. / Worley, S. / Monzingo, A.F. / Ernst, S. / Robertus, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hq6.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hq6.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hq6_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 1hq6_full_validation.pdf.gz | 461.2 KB | Display | |
Data in XML | 1hq6_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 1hq6_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/1hq6 ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hq6 | HTTPS FTP |
-Related structure data
Related structure data | 1pyaS 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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Details | THE ENZYME IS A TRIMER OF *AB* SUBUNITS. TWO TRIMERS, RELATED BY A TWO-FOLD ROTATION, CAN FORM A HEXAMER. EACH *AB* SUBUNIT CONTAINS TWO CHAINS RESULTING FROM AN AUTOCATALYTIC CLEAVAGE REACTION. THE BETA CHAIN IS RESIDUES 1 THROUGH 81, WHILE THE ALPHA CHAIN IS RESIDUES 82 THROUGH 310. RESIDUE PVL 82 IS AN N-TERMINAL PYRUVOYL GROUP USED AS A COFACTOR. EACH COMPLETE *AB* SUBUNIT CONSISTS OF A BETA CHAIN AND A PVL COFACTOR LINKED TO THE N TERMINUS OF AN ALPHA CHAIN. / TWO "AB" SUBUNITS, RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD ROTATION IN A TAIL-TO-TAIL MANNER, CONSTITUTE THE ASYMMETRIC UNIT. THIS REPRESENTS ONE-THIRD OF THE BIOLOGICAL HEXAMER. / THE SECOND ONE-THIRD OF THE HEXAMER IS ASSEMBLED BY APPLYING THE CRYSTALLOGRAPHIC THREE-FOLD OPERATOR: -Y, X-Y, Z / THE THIRD ONE-THIRD OF THE HEXAMER IS ASSEMBLED BY APPLYING THE CRYSTALLOGRAPHIC THREE-FOLD OPERATOR: Y-X, -X, Z |
-Components
#1: Protein | Mass: 8850.832 Da / Num. of mol.: 2 / Fragment: BETA CHAIN (RESIDUES 1-81) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus sp. (bacteria) / Strain: 30A / Gene: HDCA / Production host: Escherichia coli (E. coli) / References: UniProt: P00862, histidine decarboxylase #2: Protein | Mass: 25285.375 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN (RESIDUES 82-310) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus sp. (bacteria) / Strain: 30A / Gene: HDCA / Production host: Escherichia coli (E. coli) / References: UniProt: P00862, histidine decarboxylase #3: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.61 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 400, PEG 4000, TRIS-HCL, SODIUM ACETATE, N-DODECYL-BETA-N-MALTOSIDE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 13, 1999 |
Radiation | Monochromator: double focussing mirrors (Ni & Pt) + Ni filter Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 17625 / Num. obs: 17625 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.211 / % possible all: 98.8 |
Reflection shell | *PLUS % possible obs: 98.8 % / Mean I/σ(I) obs: 7.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PYA Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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