+Open data
-Basic information
Entry | Database: PDB / ID: 1h5y | ||||||
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Title | HisF protein from Pyrobaculum aerophilum | ||||||
Components | HISF | ||||||
Keywords | HISTIDINE BIOSYNTHESIS / TIM-BARREL | ||||||
Function / homology | Function and homology information imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm Similarity search - Function | ||||||
Biological species | PYROBACULUM AEROPHILUM (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Banfield, M.J. / Lott, J.S. / McCarthy, A.A. / Baker, E.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of Hisf, a Histidine Biosynthetic Protein from Pyrobaculum Aerophilum Authors: Banfield, M.J. / Lott, J.S. / Arcus, V. / Mccarthy, A.A. / Baker, E.N. #1: Journal: Science / Year: 2000 Title: Structural Evidence for Evolution of the Beta/Alpha Barrel Scaffold by Gene Duplication and Fusion Authors: Lang, D. / Thoma, R. / Henn-Sax, M. / Sterner, R. / Wilmanns, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" ON SHEET RECORDS BELOW IS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h5y.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h5y.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 1h5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h5y_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 1h5y_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 1h5y_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 1h5y_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/1h5y ftp://data.pdbj.org/pub/pdb/validation_reports/h5/1h5y | HTTPS FTP |
-Related structure data
Related structure data | 1thfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.054498, 0.998325, -0.019398), Vector: |
-Components
#1: Protein | Mass: 27010.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RESIDUES 1-3 OF THE INTACT SEQUENCE ARE NOT PRESENT IN THE EXPRESSED PROTEIN Source: (gene. exp.) PYROBACULUM AEROPHILUM (archaea) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21 / References: UniProt: Q8ZY16*PLUS #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | PROTEIN IDENTIFIED | |
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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: 4.26 Å3/Da / Density % sol: 65.5 % | ||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 10MG/ML PROTEIN IN 50MM TRIS PH 7.5, 150MM NACL. 100MM SODIUM CITRATE (PH5.6), 0.9-1.0M AMMONIUM PHOSPHATE. | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||
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: BL9-2 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 59658 / % possible obs: 98.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.7 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 25 Å |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1THF Resolution: 2→25 Å / SU B: 3.25009 / SU ML: 0.09364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.12492 Details: N-TERMINAL RESIDUES HIS-A2, MET-A3, SER-B1, HIS-B2, MET-3 ARE CLONING ARTEFACTS DERIVED FROM THE HIS-TAG, BUT ARE OBSERVED IN THE ELECTRON DENSITY. THE EXPRESSED PROTEIN COMPRISED RESIDUES ...Details: N-TERMINAL RESIDUES HIS-A2, MET-A3, SER-B1, HIS-B2, MET-3 ARE CLONING ARTEFACTS DERIVED FROM THE HIS-TAG, BUT ARE OBSERVED IN THE ELECTRON DENSITY. THE EXPRESSED PROTEIN COMPRISED RESIDUES ALA-4 - ILE-253 OF THE NATIVE HISF SEQUENCE. THE FOLLOWING RESIDUES HAVE BEEN MODELLED IN ALTERNATE CONFORMATIONS: ARG-A30, ARG-A121, ASP- A222 ARG-B30, ASP-222 RESIDUES ARG-B111 AND ARG-B121 HAVE NO INTERPRETABLE SIDE-CHAIN ELECTRON DENSITY FOR THE FOLLWOING ATOMS, WHICH HAVE BEEN SET TO ZERO OCCUPANCY: ARG-B111: CG, CD, NE, CZ, NH1, NH2 ARG-B121: CD, NE, CZ, NH1, NH2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.09 Å / Rfactor Rfree: 0.29 / Rfactor obs: 0.24 |