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- PDB-1gtk: Time-resolved and static-ensemble structural chemistry of hydroxy... -
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Basic information
Entry | Database: PDB / ID: 1gtk | ||||||
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Title | Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase | ||||||
![]() | PORPHOBILINOGEN DEAMINASE | ||||||
![]() | TRANSFERASE / BIOSYNTHESIS OF LINEAR TETRAPYRROLE / ALL ALPHA/BETA | ||||||
Function / homology | ![]() tetrapyrrole biosynthetic process / hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Helliwell, J.R. / Nieh, Y.P. / Raftery, J. / Cassetta, A. / Habash, J. / Carr, P.D. / Ursby, T. / Wulff, M. / Thompson, A.W. / Niemann, A.C. / Haedener, A. | ||||||
![]() | ![]() Title: Time-Resolved and Static-Ensemble Structural Chemistry of Hydroxymethylbilane Synthase Authors: Helliwell, J.R. / Nieh, Y.P. / Habash, J. / Faulder, P.F. / Raftery, J. / Cianci, M. / Wulff, M. / Hadener, A. #1: ![]() Title: Time-Resolved Structures of Hydroxymethylbilane Synthase (Lys59Gln Mutant) as It is Loaded with Substrate in the Crystal Determined by Laue Diffraction Authors: Helliwell, J.R. / Nieh, Y.P. / Raftery, J. / Cassetta, A. / Habash, J. / Carr, P.D. / Ursby, T. / Wulff, M. / Thompson, A.W. / Niemann, A.C. / Hadener, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80 KB | Display | ![]() |
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PDB format | ![]() | 57.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 848 KB | Display | ![]() |
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Full document | ![]() | 855.5 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ypnS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 33891.805 Da / Num. of mol.: 1 / Fragment: THREE DOMAINS Source method: isolated from a genetically manipulated source Details: CONTAINS A DIPYRROMETHANE COFACTOR LINKED TO CYSTEINE 242 Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-DPM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 50 % Description: THE STRUCTURE WAS ALREADY DETERMINED BUT REFINED HERE ONLY |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.3 Details: PROTEIN WAS CRYSTALLISED AT PH 5.3 IN SITTING DROPS OF 0.05 ML WITH 6-7 MG/ML OF PROTEIN, 0.3 MM EDTA, 15 MM DITHIOTHREITOL, 10%(W/V) PEG6000 AND 0.01% NAN3 IN 0.1 M SODIUM ACETATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Jun 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8611 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→43.85 Å / Num. obs: 34417 / % possible obs: 87 % |
Reflection shell | Resolution: 1.66→1.75 Å / % possible all: 70.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YPN Resolution: 1.66→43.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.946 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ASYMMETRIC UNIT OF THIS STRUCTURE IS NOT COMPLETE.RESIDUES 1-2, 43-59 ARE MISSING IN THE ENTRY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→43.85 Å
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Refine LS restraints |
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