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Yorodumi- PDB-2h5d: 0.9A resolution crystal structure of alpha-lytic protease complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h5d | |||||||||
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Title | 0.9A resolution crystal structure of alpha-lytic protease complexed with a transition state analogue, MeOSuc-Ala-Ala-Pro-Val boronic acid | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / A-LYTIC PROTEASE / SERINE PROTEASE / ACYLATION TRANSITION STATE / CATALYSIS / PROTEIN FOLDING / PROTEIN STABILITY / PACKING DISTORTION / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | Lysobacter enzymogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / REFINEMENT OF PREVIOUSLY-SOLVED STRUCTURE OF ALPHA-LYTIC PROTEASE BOUND TO MEOSUC-ALA-ALA-PRO-ALA BORONIC ACID / Resolution: 0.9 Å | |||||||||
Authors | Fuhrmann, C.N. / Agard, D.A. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2006 Title: Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis Authors: Fuhrmann, C.N. / Daugherty, M.D. / Agard, D.A. #1: Journal: J.Mol.Biol. / Year: 2004 Title: The 0.83A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain Authors: Fuhrmann, C.N. / Kelch, B.A. / Ota, N. / Agard, D.A. #2: Journal: Biochemistry / Year: 1989 Title: Structural analysis of specificity: alpha-lytic protease complexes with analogues of reaction intermediates Authors: Bone, R. / Frank, D. / Kettner, C.A. / Agard, D.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h5d.cif.gz | 153.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h5d.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 2h5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h5d_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 2h5d_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 2h5d_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 2h5d_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/2h5d ftp://data.pdbj.org/pub/pdb/validation_reports/h5/2h5d | HTTPS FTP |
-Related structure data
Related structure data | 2h5cC 1p02S C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19875.131 Da / Num. of mol.: 1 / Fragment: MATURE PROTEASE DOMAIN (RESIDUES 200-397) / Source method: isolated from a natural source / Details: gene alpha-LP / Source: (natural) Lysobacter enzymogenes (bacteria) / Secretion: SECRETED BY THE NATIVE BACTERIUM / References: UniProt: P00778, alpha-lytic endopeptidase | ||||||
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#2: Protein/peptide | | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Nonpolymer details | GLYCEROL BOUND TO THE CATALYTIC ADDUCT, CREATING A MIMIC OF THE ACYLATION TRANSITION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 298 K / pH: 8 Details: 1.3M LITHIUM SULFATE, 0.02M TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.75 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2004 |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→28.5 Å / Num. obs: 147100 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 0.9→0.91 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.8 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: REFINEMENT OF PREVIOUSLY-SOLVED STRUCTURE OF ALPHA-LYTIC PROTEASE BOUND TO MEOSUC-ALA-ALA-PRO-ALA BORONIC ACID Starting model: SAME PROTEIN BOUND TO MEOSUC-ALA-ALA-PRO-ALA BORONIC ACID AT 0.9A RESOLUTION (UNPUBLISHED DATA, BUT RELATED TO 1P02) Resolution: 0.9→20 Å / Num. parameters: 20128 / Num. restraintsaints: 23688 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: HYDROGEN ATOMS WERE INCLUDED IN THE REFINEMENT AS "RIDING HYDROGENS", WITH POSITION AND GEOMETRY FIXED TO THOSE VALUES DEFINED BY SHELXL-97. METHYL AND HYDROXYL HYDROGENS ON SINGLE-CONFORMER ...Details: HYDROGEN ATOMS WERE INCLUDED IN THE REFINEMENT AS "RIDING HYDROGENS", WITH POSITION AND GEOMETRY FIXED TO THOSE VALUES DEFINED BY SHELXL-97. METHYL AND HYDROXYL HYDROGENS ON SINGLE-CONFORMER SIDECHAINS WERE EACH POSITIONED AT A TORSION ANGLE THAT BEST SATISFIED POSITIVE DIFFERENCE ELECTRON DENSITY (USING INSTRUCTIONS HFIX 137 AND HFIX 147, RESPECTIVELY). IT SHOULD BE NOTED THAT THE LENGTH OF DONOR-HYDROGEN BONDS IN THIS STRUCTURE ARE LIKELY SHORTER THAN THEIR TRUE INTERNUCLEAR DISTANCE; THESE BOND LENGTHS ARE DEFINED BY SHELXL-97 PARAMETERS. THE POSITIONS OF SEVEN HYDROGEN ATOMS WERE ALLOWED TO REFINE FREELY: HIS57 HD1, HIS57 HE1, HIS57 HE2, SER214 HG, SER195 HN, GLY193 HN, AND B2V203 H1. DURING THE FINAL STAGES OF REFINEMENT, GEOMETRICAL RESTRAINTS WERE RELEASED FOR ALL NON- HYDROGEN ATOMS IN RESIDUES WITH SINGLE CONFORMATIONS. THE BORON IN RESIDUE B2V WAS REFINED AS A CARBON ATOM, ALLOWING REFINEMENT OF THE OCCUPANCY OF THIS ATOM TO ESTIMATE THE ELECTRON CONTENT (AND NEGATIVE CHARGE) AT THIS LOCATION. TO AID THE READER IN ANALYZING THE STRUCTURE IN THIS PDB FILE, THE ATOM HAS BEEN RE-NAMED TO "B", AND THE OCCUPANCY OF THE BORON ATOM MANUALLY CHANGED TO THE CORRESPONDING OCCUPANCY (1.07; REFINEMENT OF A CARBON IN THIS POSITION RESULTED IN AN OCCUPANCY OF 0.89). SEE PUBLICATION FOR MORE DETAILS.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 21 / Occupancy sum hydrogen: 1367.28 / Occupancy sum non hydrogen: 1784.32 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→20 Å
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Refine LS restraints |
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