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Yorodumi- PDB-2z2p: Crystal Structure of catalytically inactive H270A virginiamycin B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z2p | ||||||||||||
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Title | Crystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with Quinupristin | ||||||||||||
Components |
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Keywords | LYASE/ANTIBIOTIC / QUINUPRISTIN / DALFOPRISTIN / STREPTOGRAMIN / SYNERCID / LYASE-ANTIBIOTIC COMPLEX / ANTIBIOTIC RESISTANCE / ANTIBIOTIC / VIRGINIAMYCIN B LYASE / VIRGINIAMYCIN B HYDROLASE | ||||||||||||
Function / homology | Function and homology information carbon-oxygen lyase activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / antibiotic catabolic process / outer membrane-bounded periplasmic space / response to antibiotic / magnesium ion binding Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) STREPTOMYCES GRAMINOFACIEN (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||||||||
Authors | Korczynska, M. / Berghuis, A.M. | ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Structural Basis for Streptogramin B Resistance in Staphylococcus Aureus by Virginiamycin B Lyase Authors: Korczynska, M. / Mukhtar, T.A. / Wright, G.D. / Berghuis, A.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z2p.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z2p.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 2z2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z2p_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2z2p_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2z2p_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 2z2p_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/2z2p ftp://data.pdbj.org/pub/pdb/validation_reports/z2/2z2p | HTTPS FTP |
-Related structure data
Related structure data | 2z2nSC 2z2oC S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 2 / Auth seq-ID: 2 - 294 / Label seq-ID: 2 - 294
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-Components
#1: Protein | Mass: 33034.242 Da / Num. of mol.: 2 / Mutation: H270A Source method: isolated from a genetically manipulated source Details: 1. SEQUENCE FOR RESIDUES 211 AND 212 WAS DERIVED FROM THE ORIGINAL GENE. 2. RESIDUES 51 TO 56 [PLPTPD] WERE REPLACED TO DISRUPT CRYSTAL PACKING INTERACTIONS BY A CORRESPONDING LOOP, RESIDUES 135-140 [ELPNKG]. Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: BM30002, PIP524 / Gene: vgb, vgh / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) References: UniProt: P17978, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases #2: Protein/peptide | Type: Oligopeptide / Class: Antibiotic / Mass: 1024.236 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: QUINUPRISTIN IS A CYLIC HEPTAPEPTIDE. THE RING GENERATED BY LINKING RESIDUE 2 SIDE-CHAIN IS AND MAIN-CHAIN RESIDUE 7. Source: (synth.) STREPTOMYCES GRAMINOFACIEN (bacteria) / References: Quinupristin #3: Chemical | ChemComp-MG / #4: Chemical | Compound details | QUINUPRIST | |
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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: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | pH: 7.5 Details: 100MM MES BUFFER (PH 6.5), 20%(W/V) PEG 10000, PROTEIN SOLUTION SUPPLEMENTED WITH 3MM MGCL2, 3MM DALFOPRISTIN, 1MM QUINUPRISTIN, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 14813 / % possible obs: 91.1 % / Redundancy: 4.1 % / Rsym value: 0.136 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.8→2.99 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.31 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z2N Resolution: 2.8→36.18 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.858 / SU B: 38.266 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R Free: 0.578 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 20.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→36.18 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 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.95 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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