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Yorodumi- PDB-6nlr: Crystal structure of the putative histidinol phosphatase hisK fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nlr | ||||||
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Title | Crystal structure of the putative histidinol phosphatase hisK from Listeria monocytogenes with trinuclear metals determined by PIXE revealing sulphate ion in active site. Based on PIXE analysis and original date from 3DCP | ||||||
Components | Histidinol-phosphatase | ||||||
Keywords | HYDROLASE / HISTIDINOL PHOSPHATASE / HISK / HISTIDINE BIOSYNTHESIS / NESG / LMR14 / PIXE / TRINUCLEAR / SULPHATE | ||||||
Function / homology | Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / : / : / : / : Function and homology information | ||||||
Biological species | Listeria monocytogenes serotype 4b str. H7858 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Snell, E.H. / Garman, E.F. / Lowe, E.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application. Authors: Grime, G.W. / Zeldin, O.B. / Snell, M.E. / Lowe, E.D. / Hunt, J.F. / Montelione, G.T. / Tong, L. / Snell, E.H. / Garman, E.F. | ||||||
History |
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Remark 0 | THIS ENTRY 6NLR REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3DCP, DETERMINED BY S.M. ...THIS ENTRY 6NLR REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3DCP, DETERMINED BY S.M.VOROBIEV,M.SU,J.SEETHARAMAN,L.ZHAO,L.MAO,E.L.FOOTE,R.XIAO,R.NAIR,M.C.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nlr.cif.gz | 345.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nlr.ent.gz | 296.1 KB | Display | PDB format |
PDBx/mmJSON format | 6nlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nlr_validation.pdf.gz | 459.8 KB | Display | wwPDB validaton report |
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Full document | 6nlr_full_validation.pdf.gz | 462.4 KB | Display | |
Data in XML | 6nlr_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 6nlr_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/6nlr ftp://data.pdbj.org/pub/pdb/validation_reports/nl/6nlr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 32847.547 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serotype 4b str. H7858 (bacteria) Gene: hisk, DYZ35_00104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) + MAGIC / References: UniProt: A0A3A6YEN9, histidinol-phosphatase |
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-Non-polymers , 6 types, 543 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.58 Å3/Da / Density % sol: 52.23 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3DCP. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 15% PEG 8000, 0.17 M SODIUM ACETATE, 0.01 M L-CYSTEINE, 0.1 M MES PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97931 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2008 / Details: FLAT COLLIMATING MIRROR, TOROID, FOCUSING MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.6 Å / Num. obs: 114574 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 12134 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→41.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.658 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.275 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→41.6 Å
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Refine LS restraints |
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