+Open data
-Basic information
Entry | Database: PDB / ID: 4d1n | ||||||
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Title | Structure of human nNOS heme domain with L-Arg bound | ||||||
Components | NITRIC OXIDE SYNTHASE, BRAIN | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information positive regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of calcium ion transport into cytosol / Nitric oxide stimulates guanylate cyclase / myoblast fusion / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / regulation of cardiac muscle contraction by calcium ion signaling / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel ...positive regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of calcium ion transport into cytosol / Nitric oxide stimulates guanylate cyclase / myoblast fusion / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / regulation of cardiac muscle contraction by calcium ion signaling / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / peptidyl-cysteine S-nitrosylation / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / negative regulation of calcium ion transport / negative regulation of serotonin uptake / calcium channel regulator activity / regulation of cardiac muscle contraction / nitric-oxide synthase (NADPH) / sodium channel regulator activity / nitric oxide mediated signal transduction / multicellular organismal response to stress / nitric-oxide synthase activity / xenobiotic catabolic process / arginine catabolic process / striated muscle contraction / regulation of sodium ion transport / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to hormone / cell redox homeostasis / sarcoplasmic reticulum / muscle contraction / cell periphery / sarcolemma / cellular response to growth factor stimulus / vasodilation / calcium-dependent protein binding / FMN binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / flavin adenine dinucleotide binding / response to heat / scaffold protein binding / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / cytoskeleton / calmodulin binding / response to hypoxia / membrane raft / synapse / heme binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of Human Constitutive Nitric Oxide Synthases Authors: Li, H. / Jamal, J. / Plaza, C. / Pineda, S.H. / Chreifi, G. / Jing, Q. / Cinelli, M.A. / Silverman, R.B. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d1n.cif.gz | 703.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d1n.ent.gz | 584.8 KB | Display | PDB format |
PDBx/mmJSON format | 4d1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d1n_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4d1n_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4d1n_validation.xml.gz | 71.2 KB | Display | |
Data in CIF | 4d1n_validation.cif.gz | 98.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/4d1n ftp://data.pdbj.org/pub/pdb/validation_reports/d1/4d1n | HTTPS FTP |
-Related structure data
Related structure data | 4d1oC 4d1pC 1om4S C: citing same article (ref.) 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 , 1 types, 4 molecules ABCD
#1: Protein | Mass: 48655.316 Da / Num. of mol.: 4 / Fragment: RESIDUES 302-721 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29475 |
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-Non-polymers , 6 types, 877 molecules
#2: Chemical | ChemComp-ARG / #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-H4B / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | L-ARGININE (LRG): SUBSTRATE OF NOS |
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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: 3.22 Å3/Da / Density % sol: 61.8 % / Description: RPIM 0.446 CC ONE HALF 0.666 |
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Crystal grow | pH: 5 Details: 11-13% PEG3350, 50MM CITRIC ACID 50MM BIS-TRIS-PROPANE, 10% GLYCEROL, 5 MM TCEP, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2013 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. obs: 149877 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 25.42 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.8 / % possible all: 92 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OM4 Resolution: 2.03→46.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.285 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 344 TO 352 ARE DISORDERED IN CHAINS B AND D ARE DISORDERED
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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: 44.583 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→46.6 Å
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