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Yorodumi- PDB-3kw3: Crystal structure of alanine racemase from Bartonella henselae wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kw3 | ||||||
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Title | Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate | ||||||
Components | Alanine racemase | ||||||
Keywords | ISOMERASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / iodide soak / alanine racemase / LLP / cat-scratch disease | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Bartonella henselae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / MAD / molecular replacement / Resolution: 2.04 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2011 Title: SAD phasing using iodide ions in a high-throughput structural genomics environment. Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kw3.cif.gz | 156 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kw3.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/3kw3 ftp://data.pdbj.org/pub/pdb/validation_reports/kw/3kw3 | HTTPS FTP |
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-Related structure data
Related structure data | 3k9gC 3km3C 3luzC 3menC 3njbC 3o2eC 3oibC 3p96C 3pfdC 3pm6C 2dy3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41562.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: alr, BH12810 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) References: UniProt: Q6G2F2, UniProt: A0A0H3LZE4*PLUS, alanine racemase #2: 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: 2.22 Å3/Da / Density % sol: 44.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Native crystal grown in 0.1 M Hepes pH 8.0, 33% PEG 3350 at 42.3 mg/mL, crystal tracking ID 203636d11; crystal used for combined Phaser MR/IodoSAD grown in 0.1 M Hepes pH 8.5, 0.2 M MgCl2, ...Details: Native crystal grown in 0.1 M Hepes pH 8.0, 33% PEG 3350 at 42.3 mg/mL, crystal tracking ID 203636d11; crystal used for combined Phaser MR/IodoSAD grown in 0.1 M Hepes pH 8.5, 0.2 M MgCl2, 25% PEG 3350 and soaked for 1 hour in 0.1 M Hepes pH 8.0, 1.0 M KI, 35% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-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 | Redundancy: 5.3 % / Av σ(I) over netI: 17.45 / Number: 114922 / Rmerge(I) obs: 0.088 / Χ2: 1.04 / D res high: 2.95 Å / Num. obs: 29953 / % possible obs: 99.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell | ID: 1
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Reflection | Resolution: 2.04→50 Å / Num. obs: 45971 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.088 / Χ2: 1.037 / Net I/σ(I): 17.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.04→2.12 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.79 / Num. unique all: 4405 / Χ2: 1.032 / % possible all: 96.7 |
-Phasing
Phasing |
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-Processing
Software |
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Refinement | Method to determine structure: SAD, molecular replacement Starting model: 2DY3 Resolution: 2.04→34.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.824 / SU B: 10.904 / SU ML: 0.13 / SU R Cruickshank DPI: 0.216 / SU Rfree: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.97 Å2 / Biso mean: 22.817 Å2 / Biso min: 8.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→34.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.097 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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