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Yorodumi- PDB-1qq7: STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qq7 | ||||||
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Title | STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS WITH CHLOROPROPIONIC ACID COVALENTLY BOUND | ||||||
Components | PROTEIN (L-2-HALOACID DEHALOGENASE) | ||||||
Keywords | HYDROLASE / L-2-HALOACID DEHALOGENASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Xanthobacter autotrophicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase. Authors: Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W. #1: Journal: J.Biol.Chem. / Year: 1997 Title: Three-Dimensional Structure of L-2-Haloacid Dehalogenase from Xanthobacter Autotrophicus Gj10 Complexed with the Substrate-Analogue Formate Authors: Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Janssen, D.B. / Dijkstra, B.W. #2: Journal: Protein Sci. / Year: 1995 Title: Crystallization and Preliminary X-Ray Analysis of L-2-Haloacid Dehalogenase from Xanthobacter Autotrophicus Gj10 Authors: Ridder, I.S. / Rozeboom, H.J. / Kingma, J. / Janssen, D.B. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qq7.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qq7.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qq7 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qq7 | HTTPS FTP |
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-Related structure data
Related structure data | 1qq5C 1qq6C 1qqyS 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
#1: Protein | Mass: 27582.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: 2-CHLOROPROPIONIC ACID MOIETY COVALENTLY BOUND TO ASP 8 IN ACTIVE SITES OF BOTH CHAINS Source: (natural) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / References: UniProt: Q60099, (S)-2-haloacid dehalogenase #2: Chemical | #3: 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 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: seeding, Ridder, I.S., (1995) Protein Sci., 4, 2619. PH range low: 7 / PH range high: 6.8 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 12, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→99 Å / Num. obs: 47721 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.145 / % possible all: 84.1 |
Reflection | *PLUS Num. measured all: 202654 |
Reflection shell | *PLUS % possible obs: 84.1 % / Mean I/σ(I) obs: 7 |
-Processing
Software |
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Refinement | Starting model: 1QQY Resolution: 1.7→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: ENGH & HUBER CNS FORCE CONSTANT ON OMEGA DIHEDRAL ANGLE SET TO 20 % OF ORIGINAL VALUE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 75.08 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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