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Yorodumi- PDB-2w8s: CRYSTAL STRUCTURE OF A catalytically promiscuous PHOSPHONATE MONO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w8s | ||||||
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Title | CRYSTAL STRUCTURE OF A catalytically promiscuous PHOSPHONATE MONOESTER HYDROLASE FROM Burkholderia caryophylli | ||||||
Components | PHOSPHONATE MONOESTER HYDROLASE | ||||||
Keywords | HYDROLASE / FORMYLGLYCINE / PHOSPHODIESTERASE / ALKALINE PHOSPHATASE SUPERFAMILY / CATALYTIC PROMISCUITY / PHOSPHONATE MONOESTER HYDROLASE | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / sulfuric ester hydrolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / Hydrolases; Acting on ester bonds / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | BURKHOLDERIA CARYOPHYLLI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Jonas, S. / van Loo, B. / Hyvonen, M. / Hollfelder, F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: An Efficient, Multiply Promiscuous Hydrolase in the Alkaline Phosphatase Superfamily. Authors: Van Loo, B. / Jonas, S. / Babtie, A.C. / Benjdia, A. / Berteau, O. / Hyvonen, M. / Hollfelder, F. #1: Journal: J.Mol.Biol. / Year: 2008 Title: A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium Leguminosarum. Authors: Jonas, S. / Van Loo, B. / Hyvonen, M. / Hollfelder, F. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w8s.cif.gz | 425.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w8s.ent.gz | 346.4 KB | Display | PDB format |
PDBx/mmJSON format | 2w8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w8s_validation.pdf.gz | 507.9 KB | Display | wwPDB validaton report |
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Full document | 2w8s_full_validation.pdf.gz | 538.2 KB | Display | |
Data in XML | 2w8s_validation.xml.gz | 81.2 KB | Display | |
Data in CIF | 2w8s_validation.cif.gz | 114.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/2w8s ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w8s | HTTPS FTP |
-Related structure data
Related structure data | 2vqrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 6
NCS ensembles :
NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 61220.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: AT POSITION 57 OF THE PROTEIN CHAINS A, B, C, D. BOTH CYS AND FGL ARE PRESENT AT 0.80 AND 0.20 OCCUPANCIES, RESPECTIVELY. Source: (gene. exp.) BURKHOLDERIA CARYOPHYLLI (bacteria) / Strain: BG2952 / Plasmid: PASK-IBA5PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q45087 |
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-Non-polymers , 5 types, 837 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 2-AMINOPROPANEDIOIC ACID (FGL): THE MODIFICATION IS INCOMPLETE. ZINC ION (ZN): NATURE AND OCCUPANCY ...2-AMINOPROPA |
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Sequence details | RESIDUES 1-29 IN THE PROTEIN SEQUENCE ORIGINATE FROM THE STREP-TAG AND LINKER. AT POSITION 57 OF ...RESIDUES 1-29 IN THE PROTEIN SEQUENCE ORIGINATE FROM THE STREP-TAG AND LINKER. AT POSITION 57 OF THE PROTEIN CHAINS A, B, C, D. BOTH CYS AND FGL ARE PRESENT AT 0.80 AND 0.20 OCCUPANCIE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M MES PH 6.5, 20 % (W/V) PEG 5000 MME, 0.3 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 4, 2006 / Details: CONFOCAL MAXFLUX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.62 Å / Num. obs: 96059 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.49 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.52 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VQR Resolution: 2.4→48.62 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 20.292 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.255 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→48.62 Å
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Refine LS restraints |
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