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Yorodumi- PDB-2czl: Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2czl | ||||||
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Title | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 (Cys11 modified with beta-mercaptoethanol) | ||||||
Components | hypothetical protein TTHA1568 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein / TTHA1568 / Extremely thermophilic bacteria / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information 5,8-dihydroxy-2-naphthoate synthase / carbon-carbon lyase activity / menaquinone biosynthetic process Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å | ||||||
Authors | Arai, R. / Nishino, A. / Nagano, K. / Kamo-Uchikubo, T. / Nishimoto, M. / Toyama, M. / Terada, T. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2009 Title: Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8. Authors: Arai, R. / Murayama, K. / Uchikubo-Kamo, T. / Nishimoto, M. / Toyama, M. / Kuramitsu, S. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2czl.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2czl.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 2czl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2czl_validation.pdf.gz | 753.9 KB | Display | wwPDB validaton report |
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Full document | 2czl_full_validation.pdf.gz | 755.7 KB | Display | |
Data in XML | 2czl_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 2czl_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/2czl ftp://data.pdbj.org/pub/pdb/validation_reports/cz/2czl | HTTPS FTP |
-Related 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
#1: Protein | Mass: 30144.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1568 / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 55981537, UniProt: Q5SI12*PLUS |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-TLA / |
#4: Chemical | ChemComp-XPE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-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: 1.55→50 Å / Num. obs: 45583 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.071 / Net I/σ(I): 18.79 | ||||||||||||||||||
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5.05 / Num. unique all: 4258 / Rsym value: 0.282 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.55→42.82 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 670101.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.8724 Å2 / ksol: 0.368804 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→42.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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