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Yorodumi- PDB-3h8t: Structure of Porphyromonas gingivalis heme-binding protein HmuY i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h8t | ||||||
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Title | Structure of Porphyromonas gingivalis heme-binding protein HmuY in complex with Heme | ||||||
Components | HmuY | ||||||
Keywords | heme-binding protein / hemophore / bacterial virulence factor / periodontitis | ||||||
Function / homology | HmuY protein / HmuY protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / HmuY Function and homology information | ||||||
Biological species | Porphyromonas gingivalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å | ||||||
Authors | Wojtowicz, H. / Guevara, T. / Tallant, C. / Olczak, M. / Sroka, A. / Potempa, J. / Sola, M. / Olczak, T. / Gomis-Ruth, F.X. | ||||||
Citation | Journal: Plos Pathog. / Year: 2009 Title: Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis Authors: Wojtowicz, H. / Guevara, T. / Tallant, C. / Olczak, M. / Sroka, A. / Potempa, J. / Sola, M. / Olczak, T. / Gomis-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h8t.cif.gz | 184.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h8t.ent.gz | 146.4 KB | Display | PDB format |
PDBx/mmJSON format | 3h8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h8t_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3h8t_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3h8t_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 3h8t_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/3h8t ftp://data.pdbj.org/pub/pdb/validation_reports/h8/3h8t | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21227.529 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26 TO 216 (26 to 34 disordered) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: HmuY, hmuY' / Production host: Escherichia coli (E. coli) / References: UniProt: A2I2W2 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Crystallization assays were performed following the sitting-drop vapor diffusion method. Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on ...Details: Crystallization assays were performed following the sitting-drop vapor diffusion method. Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Wilden / Innovadyne) by a Cartesian nanodrop robot (Genomic Solutions) at the joint IBMB-CSIC/IRB/Barcelona Science Park High-Throughput Crystallography Platform (PAC). Best crystals as thin reddish prisms appeared in a Bruker steady-temperature crystal farm at 20 C using protein solution (26mg/mL in 5mM Tris/HCl, pH 8.0) and 2.4M (NH4)2SO4, 0.1M MES, pH6.0 as reservoir solution and D(+)-glucose monohydrate as additive (relative volumetric ratios 1:1:0.35). These conditions were successfully scaled up to the microliter range with Cryschem crystallization dishes (Hampton Research). VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.8→48.6 Å / Num. all: 47598 / Num. obs: 47598 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.6 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.8→48.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.29 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 14.133 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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