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Yorodumi- PDB-1o4t: Crystal structure of a predicted oxalate decarboxylase (tm1287) f... -
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-Basic information
Entry | Database: PDB / ID: 1o4t | ||||||
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Title | Crystal structure of a predicted oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 A resolution | ||||||
Components | putative oxalate decarboxylase | ||||||
Keywords | LYASE / Double-stranded beta-helix fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information oxalate decarboxylase activity / oxalate metabolic process / manganese ion binding / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution Authors: Schwarzenbacher, R. / von Delft, F. / Jaroszewski, L. / 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. / von Delft, F. / Jaroszewski, L. / 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 | 1o4t.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o4t.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 1o4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/1o4t ftp://data.pdbj.org/pub/pdb/validation_reports/o4/1o4t | 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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Unit cell |
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-Components
#1: Protein | Mass: 14750.821 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1287 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X113 #2: Chemical | #3: Chemical | #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: 2.55 Å3/Da / Density % sol: 51.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 6 Details: 20 % PEG 6000, 1.0 M LiCl, 0.1 M MES, pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: BL9-1 / Wavelength: 0.983967 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 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: 0.983967 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25.29 Å / Num. obs: 17758 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 36.93 Å2 / Rsym value: 0.083 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.555 / % possible all: 88 |
Reflection | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 33.52 Å / % possible obs: 0.098 % / Num. measured all: 62794 |
Reflection shell | *PLUS % possible obs: 88 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FI2 Resolution: 1.95→25.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.542 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. METAL IDENTIFIED BY A) HOMOLOGY TO 1J58 B) BEST AGREEMENT OF REFINED B-FACTOR WITH LIGATING RESIDUES. 2. OXALATE IDENIFIED BASED ON HOMOLOGY TO 1J58. HIGH BFACTORS INDICATE PARTIAL ...Details: 1. METAL IDENTIFIED BY A) HOMOLOGY TO 1J58 B) BEST AGREEMENT OF REFINED B-FACTOR WITH LIGATING RESIDUES. 2. OXALATE IDENIFIED BASED ON HOMOLOGY TO 1J58. HIGH BFACTORS INDICATE PARTIAL OCCUPANCY, WHICH WAS NOT MODELED. C- C BOND PLANARITY WAS NOT RESTRAINED DURING REFINEMENT. 3. ARG23 HAS CLOSELY-BOUND WATER; DENSITY SUGGESTS POSSIBLE OMEGA -HYDROXYLATED ARGININE. 4. UNEXPLAINED CONTINUOUS DENSITY MODELED AS WATER CHAINS. 5. 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: 32.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→25.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 15.3219 Å / Origin y: -0.1822 Å / Origin z: 16.2354 Å
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Refinement TLS group |
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Software | *PLUS Name: REFMAC / Version: 5.1.9999 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 33.52 Å / Num. reflection obs: 17758 / % reflection Rfree: 5 % / Rfactor Rwork: 0.163 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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