+Open data
-Basic information
Entry | Database: PDB / ID: 4es7 | ||||||
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Title | crystal structure of protein HC from Homo sapiens at 2 angstrom | ||||||
Components | Protein AMBP | ||||||
Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / IgA binding / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / calcium channel inhibitor activity / Scavenging of heme from plasma / female pregnancy / serine-type endopeptidase inhibitor activity ...Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / IgA binding / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / calcium channel inhibitor activity / Scavenging of heme from plasma / female pregnancy / serine-type endopeptidase inhibitor activity / carbohydrate binding / nuclear membrane / collagen-containing extracellular matrix / mitochondrial inner membrane / blood microparticle / oxidoreductase activity / cell adhesion / heme binding / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Zhang, Y.L. / Gao, Z.Q. / Wang, D.Q. / Dong, Y.H. | ||||||
Citation | Journal: To be Published Title: crystal structure of protein HC from Home sapiens at 2 angstrom Authors: Zhang, Y.L. / Gao, Z.Q. / Wang, D.Q. / Dong, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4es7.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4es7.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 4es7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/4es7 ftp://data.pdbj.org/pub/pdb/validation_reports/es/4es7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22633.561 Da / Num. of mol.: 1 / Fragment: UNP residues 27-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMBP, HCP, ITIL / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P02760 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.2M ammonium citrate, 20% PEG 3350, 0.1M HEPES pH 6.9, 40% 1,1,1,3,3,3-Hexafluoro-z-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2011 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 9932 / Num. obs: 9932 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 30.63 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 50.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 8.57 / Num. unique all: 982 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→34.669 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.12 / σ(F): 1.34 / Phase error: 28.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.087 Å2 / ksol: 0.379 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.44 Å2 / Biso mean: 40.3096 Å2 / Biso min: 15.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→34.669 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Origin x: 14.9191 Å / Origin y: -6.7183 Å / Origin z: -9.2317 Å
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Refinement TLS group |
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