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Yorodumi- PDB-1o4u: Crystal structure of a nicotinate nucleotide pyrophosphorylase (t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o4u | ||||||
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Title | Crystal structure of a nicotinate nucleotide pyrophosphorylase (tm1645) from thermotoga maritima at 2.50 A resolution | ||||||
Components | Type II quinolic acid phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution Authors: Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. ...Authors: Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o4u.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o4u.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 1o4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/1o4u ftp://data.pdbj.org/pub/pdb/validation_reports/o4/1o4u | HTTPS FTP |
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-Related structure data
Related structure data | 1qpnS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 273 / Label seq-ID: 13 - 285
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-Components
#1: Protein | Mass: 31679.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1645 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X8 #2: 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: 3.57 Å3/Da / Density % sol: 65.25 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6 Details: 10% PEG-6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL11-1 / Wavelength: 0.972386 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2002 / Details: flat mirror |
Radiation | Monochromator: single crystal Si(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972386 Å / Relative weight: 1 |
Reflection | Resolution: 2.501→38.29 Å / Num. all: 29194 / Num. obs: 29194 / % possible obs: 99.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 63.66 Å2 / Rsym value: 0.081 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 2002 / Rsym value: 0.546 / % possible all: 93.2 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 125534 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS % possible obs: 93.2 % / Rmerge(I) obs: 0.546 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QPN Resolution: 2.5→38.29 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.677 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. UNEXPLAINED BLOB OF DENSITY AROUND RESIDUE 75 IN BOTH CHAINS, TOO LARGE AND FAR FROM RESIDUES TO BE WATER, NO METALS IN CRYSTALLIZATION SOLUTION. 2. RESIDUAL DENSITY FOR RESIDUE 209 COULD ...Details: 1. UNEXPLAINED BLOB OF DENSITY AROUND RESIDUE 75 IN BOTH CHAINS, TOO LARGE AND FAR FROM RESIDUES TO BE WATER, NO METALS IN CRYSTALLIZATION SOLUTION. 2. RESIDUAL DENSITY FOR RESIDUE 209 COULD NOT BE MODELLED WITHOUT VIOLATING RAMACHANDRAN ANGLES; BUT MODELLED CONFORMATION CORRESPONDS TO HOMOLOGUE 1QPN. 3. 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: 37.427 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→38.29 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3991 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.501→2.566 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 25.6 Å / Origin y: 22.743 Å / Origin z: 41.374 Å
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth seq-ID: 1 - 272 / Label seq-ID: 13 - 284
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Software | *PLUS Name: REFMAC / Version: 5.1.9999 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 29193 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.213 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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