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Yorodumi- PDB-1vj2: Crystal structure of a novel family of manganese-containing cupin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vj2 | |||||||||
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Title | Crystal structure of a novel family of manganese-containing cupin (tm1459) from thermotoga maritima at 1.65 A resolution | |||||||||
Components | novel manganese-containing cupin TM1459 | |||||||||
Keywords | METAL BINDING PROTEIN / Novel manganese-containing cupin / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution. Authors: Jaroszewski, L. / Schwarzenbacher, R. / von Delft, F. / McMullan, D. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / ...Authors: Jaroszewski, L. / Schwarzenbacher, R. / von Delft, F. / McMullan, D. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Levin, I. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Reyes, R. / Rezezadeh, F. / Robb, A. / Sims, E. / 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 600 | HETEROGEN THE ACTIVE SITE OF SUBUNIT A NEAR CYS106 HAS BEEN MODELED AS TYPE UNL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vj2.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vj2.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/1vj2 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/1vj2 | HTTPS FTP |
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-Related structure data
Related structure data | 1fi2S 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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-Components
#1: Protein | Mass: 14590.701 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1459 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1H0 #2: Chemical | #3: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #4: 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: 2.71 Å3/Da / Density % sol: 54.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.2 Details: 50% (v/v) PEG-200, 0.1M Phosphate-citrate pH 4.2 0.2M NaCl, pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.9 / 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: Jan 9, 2002 / Details: flat mirror |
Radiation | Monochromator: single crystal Si(311) 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: 1.65→48.13 Å / Num. all: 35029 / Num. obs: 35029 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 30.49 Å2 / Rsym value: 0.057 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 4592 / Rsym value: 0.466 / % possible all: 87.6 |
Reflection | *PLUS Highest resolution: 1.65 Å / Num. measured all: 124395 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 87.6 % / Rmerge(I) obs: 0.577 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FI2 Resolution: 1.65→33.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.097 / SU ML: 0.097 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE BOUND METAL WAS IDENTIFIED AS TRANSITION METAL BY ITS COORDINATION GEOMETRY, AND AS MANGANESE BY COMPARISON WITH THE HOMOLOGOUS ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE BOUND METAL WAS IDENTIFIED AS TRANSITION METAL BY ITS COORDINATION GEOMETRY, AND AS MANGANESE BY COMPARISON WITH THE HOMOLOGOUS STRUCTURE TM1287 (1O4T) AS WELL AS BY HAVING BEST B-FACTOR AGREEMENT WITH SURROUNDING ATOMS. 3. THE ACTIVE SITE OF SUBUNIT A NEAR CYS106 HAS BEEN MODELED AS TYPE UNL.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.615 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→33.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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Software | *PLUS Name: REFMAC / Version: 5.1.9999 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.249 / Rfactor Rwork: 0.208 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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