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Yorodumi- PDB-5g4h: 1.50 A resolution catechol (1,2-dihydroxybenzene) inhibited Sporo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g4h | ||||||
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Title | 1.50 A resolution catechol (1,2-dihydroxybenzene) inhibited Sporosarcina pasteurii urease | ||||||
Components | (UREASE SUBUNIT ...) x 3 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | SPOROSARCINA PASTEURII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Mazzei, L. / Cianci, M. / Musiani, F. / Ciurli, S. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2016 Title: Inactivation of Urease by Catechol: Kinetics and Structure. Authors: Mazzei, L. / Cianci, M. / Musiani, F. / Lente, G. / Palombo, M. / Ciurli, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g4h.cif.gz | 352.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g4h.ent.gz | 286.4 KB | Display | PDB format |
PDBx/mmJSON format | 5g4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/5g4h ftp://data.pdbj.org/pub/pdb/validation_reports/g4/5g4h | HTTPS FTP |
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-Related structure data
Related structure data | 4ac7S 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
-UREASE SUBUNIT ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 11134.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Strain: DSM 33 References: UniProt: A0A0H3YGY5, UniProt: P41022*PLUS, urease |
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#2: Protein | Mass: 13975.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Strain: DSM 33 References: UniProt: A0A0H3YLV6, UniProt: P41021*PLUS, urease |
#3: Protein | Mass: 61575.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Strain: DSM 33 / References: UniProt: A0A0H3YL32, urease |
-Non-polymers , 6 types, 700 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-CAQ / | #8: Chemical | ChemComp-OH / | #9: 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: 2.75 Å3/Da / Density % sol: 55.23 % / Description: NONE |
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Crystal grow | pH: 6.3 Details: 1.8 M AMMONIUM SULFATE, 50 MM SODIUM CITRATE BUFFER, PH 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→94.51 Å / Num. obs: 152722 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 11.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AC7 Resolution: 1.5→113.69 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.96 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.351 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→113.69 Å
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Refine LS restraints |
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