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Yorodumi- PDB-4grk: Crystal Structure of C-lobe of Bovine lactoferrin Complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4grk | |||||||||
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Title | Crystal Structure of C-lobe of Bovine lactoferrin Complexed with ketorolac at 1.68 A Resolution | |||||||||
Components |
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Keywords | HYDROLASE / Metal binding protein / NSAIDs | |||||||||
Function / homology | Function and homology information Metal sequestration by antimicrobial proteins / Antimicrobial peptides / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of lipopolysaccharide-mediated signaling pathway / specific granule / negative regulation of osteoclast development / antifungal humoral response ...Metal sequestration by antimicrobial proteins / Antimicrobial peptides / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of lipopolysaccharide-mediated signaling pathway / specific granule / negative regulation of osteoclast development / antifungal humoral response / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / Neutrophil degranulation / cysteine-type endopeptidase inhibitor activity / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / innate immune response in mucosa / recycling endosome / antibacterial humoral response / iron ion transport / early endosome / iron ion binding / signaling receptor binding / serine-type endopeptidase activity / negative regulation of apoptotic process / proteolysis / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Gautam, L. / Shukla, P.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of C-lobe of Bovine lactoferrin Complexed with ketorolac at 1.68 A Resolution Authors: Gautam, L. / Shukla, P.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4grk.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4grk.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 4grk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/4grk ftp://data.pdbj.org/pub/pdb/validation_reports/gr/4grk | HTTPS FTP |
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-Related structure data
Related structure data | 3rgyS 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 36622.312 Da / Num. of mol.: 1 / Fragment: C-lobe, UNP RESIDUES 361-695 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein/peptide | Mass: 652.759 Da / Num. of mol.: 1 / Fragment: C-lobe, UNP RESIDUES 700-705 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P24627 |
-Sugars , 3 types, 3 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 375 molecules
#6: Chemical | #7: Chemical | ChemComp-FE / | #8: Chemical | ChemComp-CO3 / | #9: Chemical | ChemComp-SO4 / | #10: Chemical | #11: Chemical | ChemComp-KTR / ( | #12: Water | ChemComp-HOH / | |
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-Details
Sequence details | THERE IS A CONFLICT BETWEEN SEQRES(LYS A 565, GLU A 608) AND SEQUENCE DATABASE (ASN, LYS). THE ...THERE IS A CONFLICT BETWEEN SEQRES(LYS A 565, GLU A 608) AND SEQUENCE DATABASE (ASN, LYS). THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT. C-LOBE OF LACTOFERRI |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.01M Znso4, 0.1M MES, 25% PEG, Monomethyl Ether 550 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 26, 2012 / Details: mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→62.57 Å / Num. obs: 43835 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.047 / Net I/σ(I): 35.4 |
Reflection shell | Resolution: 1.68→1.72 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.298 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RGY Resolution: 1.68→62.57 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.715 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.086 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 29.176 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→62.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.683→1.727 Å / Total num. of bins used: 20
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