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Yorodumi- PDB-4z8t: CRYSTAL STRUCTURE OF AvrRxo1-ORF1:AvrRxo1-ORF2 WITH SULPHATE IONS -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z8t | |||||||||||||||
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Title | CRYSTAL STRUCTURE OF AvrRxo1-ORF1:AvrRxo1-ORF2 WITH SULPHATE IONS | |||||||||||||||
Components |
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Keywords | PROTEIN BINDING / AVRRXO1-ORF2 AVRRXO1-ORF1 AVRRXO1 AVRRXO1 REQUIRED CHAPERONE 1 / EFFECTOR PROTEINS AND MOLECULAR CHAPERONE | |||||||||||||||
Function / homology | Zeta toxin domain / Zeta toxin / kinase activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ACETATE ION / AvrRxo1-ORF1 / AvrRxo1-ORF2 Function and homology information | |||||||||||||||
Biological species | Xanthomonas oryzae pv. oryzicola (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||||||||
Authors | Han, Q. / Zhou, C. / Wu, S. / Liu, Y. / Yang, Z. / Miao, J. / Triplett, L. / Cheng, Q. / Tokuhisa, J. / Deblais, L. ...Han, Q. / Zhou, C. / Wu, S. / Liu, Y. / Yang, Z. / Miao, J. / Triplett, L. / Cheng, Q. / Tokuhisa, J. / Deblais, L. / Robinson, H. / Leach, J.E. / Li, J. / Zhao, B. | |||||||||||||||
Funding support | United States, China, 4items
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Citation | Journal: Structure / Year: 2015 Title: Crystal Structure of Xanthomonas AvrRxo1-ORF1, a Type III Effector with a Polynucleotide Kinase Domain, and Its Interactor AvrRxo1-ORF2. Authors: Han, Q. / Zhou, C. / Wu, S. / Liu, Y. / Triplett, L. / Miao, J. / Tokuhisa, J. / Deblais, L. / Robinson, H. / Leach, J.E. / Li, J. / Zhao, B. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z8t.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z8t.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 4z8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z8t_validation.pdf.gz | 461.3 KB | Display | wwPDB validaton report |
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Full document | 4z8t_full_validation.pdf.gz | 466.2 KB | Display | |
Data in XML | 4z8t_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4z8t_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/4z8t ftp://data.pdbj.org/pub/pdb/validation_reports/z8/4z8t | HTTPS FTP |
-Related structure data
Related structure data | 4z8qC 4z8uC 4z8vC 4q5l C: citing same article (ref.) 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 36303.531 Da / Num. of mol.: 1 / Fragment: unp residues 88-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas oryzae pv. oryzicola (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: Q6TKR8 |
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#2: Protein | Mass: 11523.586 Da / Num. of mol.: 1 / Fragment: unp residues 1-98 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas oryzae pv. oryzicola (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: Q6TKR9 |
-Non-polymers , 4 types, 385 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-ACT / | #6: 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: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.6M (NH4)2SO4, 18% GLYCEROL, 8 MM DTT, 100 MM NA-CITRATE, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2012 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. obs: 59173 / % possible obs: 99 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.088 / Rsym value: 0.083 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.532 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4Q5L 4q5l Resolution: 1.64→45.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 30.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→45.88 Å
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Refine LS restraints |
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