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- PDB-2h1n: 3.0 A X-ray structure of putative oligoendopeptidase F: crystals ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2h1n | ||||||
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Title | 3.0 A X-ray structure of putative oligoendopeptidase F: crystals grown by vapor diffusion technique | ||||||
![]() | Oligoendopeptidase F | ||||||
![]() | HYDROLASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PSI | ||||||
Function / homology | ![]() peptide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gerdts, C.J. / Tereshko, V. / Dementieva, I. / Collart, F. / Joachimiak, A. / Kossiakoff, A. / Ismagilov, R.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Time-Controlled Microfluidic Seeding in nL-Volume Droplets To Separate Nucleation and Growth Stages of Protein Crystallization. Authors: Gerdts, C.J. / Tereshko, V. / Yadav, M.K. / Dementieva, I. / Collart, F. / Joachimiak, A. / Stevens, R.C. / Kuhn, P. / Kossiakoff, A. / Ismagilov, R.F. | ||||||
History |
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Remark 999 | SEQUENCE At the time of processing, the sequence of this protein is not available at the UNP ...SEQUENCE At the time of processing, the sequence of this protein is not available at the UNP sequence database. Residues -2 to 0 are cloning artifacts. | ||||||
Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). EACH CHAIN REPRESENTS ONE BIOLOGICAL UNIT. THE OLIGOMERIZATION IS UNKNOWN. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231 KB | Display | ![]() |
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PDB format | ![]() | 194.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.7 KB | Display | ![]() |
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Full document | ![]() | 448.7 KB | Display | |
Data in XML | ![]() | 38.1 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
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Components
#1: Protein | Mass: 66994.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GK0963 / Plasmid: PMCSG7 / Production host: ![]() ![]() References: UniProt: Q5L1D2*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | #3: Chemical | ChemComp-UNL / Num. of mol.: 6 / Source method: obtained synthetically #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Hampton research SaltRX condition #96: 0.1M Bis-Tris Propane buffer, 60% Tascimate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS. K-B GEOMETRY |
Radiation | Monochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 42052 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WE HAVE DETECTED THE DIFFERENCE ELECTRON DENSITY AT >2.5 SIGMA LEVEL IN THE CENTER GROOVE OF THE MOLECULE. WE HAVE USED TASCIMATE (THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WE HAVE DETECTED THE DIFFERENCE ELECTRON DENSITY AT >2.5 SIGMA LEVEL IN THE CENTER GROOVE OF THE MOLECULE. WE HAVE USED TASCIMATE (THE HAMPTON RESEARCH PROPRIETARY MIXTURE OF ORGANIC ACIDS) FOR CRYSTALLIZATION. IT IS LIKELY THAT ONE OF THE ORGANIC ACIDS OR THEIR MIXTURE ENTERS THE GROOVE IN THE SOLUTION AND HELPS TO STABILIZE THE CLOSED CONFORMATION OF OLIGOENDOPEPTIDASE F IN THE CRYSTAL FORM. WE DID NOT ATTEMPT TO INTERPRET THE DIFFERENCE DENSITY AND USED THE UNKNOWN LIGAND TYPE (UNL) WITH OCCUPANCY=0 IN THE COORDINATE FILE TO INDICATE THIS FACT.
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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: 63.66 Å2
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Refinement step | Cycle: LAST / Resolution: 3→20 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: 3→3.08 Å / Total num. of bins used: 20
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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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