+Open data
-Basic information
Entry | Database: PDB / ID: 2zlt | ||||||
---|---|---|---|---|---|---|---|
Title | Horse methemoglobin high salt, pH 7.0 | ||||||
Components |
| ||||||
Keywords | Oxygen storage / Oxygen transport / protein hydration / allosteric transitions / variability in quaternary structure / solvent content and crystal structure / water-mediated transformation / Heme / Iron / Metal-binding / Polymorphism / Transport | ||||||
Function / homology | Function and homology information hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kaushal, P.S. / Sankaranarayanan, R. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Water-mediated variability in the structure of relaxed-state haemoglobin Authors: Kaushal, P.S. / Sankaranarayanan, R. / Vijayan, M. #1: Journal: Proteins / Year: 2005 Title: A new relaxed state in horse methemoglobin characterized by crystallographic studies Authors: Sankaranarayanan, R. / Biswal, B.K. / Vijayan, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structures of human oxy- and deoxyhaemoglobin at different levels of humidity: variability in the T state Authors: Biswal, B.K. / Vijayan, M. #3: Journal: Curr.Sci. / Year: 2001 Title: Structure of human methaemoglobin: The variation of a theme Authors: Biswal, B.K. / Vijayan, M. #4: Journal: PROC.R.SOC.LOND A MATH.PHYS.SCI. / Year: 1954 Title: The structure of hemoglobin III: Direct determination of the molecular transform Authors: Perutz, M.F. #5: Journal: Acta Crystallogr. / Year: 1953 Title: Discontinuous lattice changes in hemoglobin crystal Authors: Huxley, H.E. / Kendrew, J.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zlt.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zlt.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zlt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2zlt_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2zlt_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 2zlt_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/2zlt ftp://data.pdbj.org/pub/pdb/validation_reports/zl/2zlt | HTTPS FTP |
-Related structure data
Related structure data | 2zluC 2zlvC 2zlwC 2zlxC 2mhbS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15138.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P01958 | ||
---|---|---|---|
#2: Protein | Mass: 16032.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02062 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.61 % |
---|---|
Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 7 Details: 2.6M ammonium sulfate, 0.01M ammonium phosphate, pH 7.0, LIQUID DIFFUSION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 2003 / Details: OSMIC MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18.32 Å / Num. obs: 26933 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2MHB Resolution: 1.9→18.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.588 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→18.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|