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- PDB-5nse: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE, H4B-FREE, HYDROXY-ARG C... -

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Basic information

Entry
Database: PDB / ID: 5nse
TitleBOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE, H4B-FREE, HYDROXY-ARG COMPLEX
ComponentsPROTEIN (NITRIC OXIDE SYNTHASE)
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / HEME PROTEIN / TETRAHYDROBIOPTERIN
Function / homology
Function and homology information


cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric-oxide synthase activity / mitochondrion organization / arginine catabolic process / nitric oxide biosynthetic process / caveola ...cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric-oxide synthase activity / mitochondrion organization / arginine catabolic process / nitric oxide biosynthetic process / caveola / FMN binding / blood coagulation / flavin adenine dinucleotide binding / NADP binding / calmodulin binding / cytoskeleton / heme binding / Golgi apparatus / metal ion binding
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 3 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, N-terminal ...Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 3 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Oxidoreductase NAD-binding domain / Oxidoreductase FAD/NAD(P)-binding / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLIC ACID / PROTOPORPHYRIN IX CONTAINING FE / N-OMEGA-HYDROXY-L-ARGININE / Nitric oxide synthase, endothelial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsRaman, C.S. / Li, H. / Martasek, P. / Masters, B.S.S. / Poulos, T.L.
Citation
Journal: To be Published
Title: Crystal Structures of the Heme Domain of Bovine Endothelial Nitric Oxide Synthase Complexed with Arginine Analogues
Authors: Raman, C.S. / Li, H. / Martasek, P. / Masters, B.S.S. / Poulos, T.L.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal Structure of Constitutive Endothelial Nitric Oxide: A Paradigm for Pterin Function Involving a Novel Metal Center
Authors: Raman, C.S. / Li, H. / Martasek, P. / Kral, V. / Masters, B.S.S. / Poulos, T.L.
#2: Journal: Science / Year: 1998
Title: Structure of Nitric Oxide Synthase Oxygenase Dimer with Pterin and Substrate
Authors: Crane, B.R. / Arvai, A.S. / Ghosh, D.K. / Wu, C. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A.
#3: Journal: Science / Year: 1997
Title: The Structure of Nitric Oxide Synthase Oxygenase Domain and Inhibitor Complex
Authors: Crane, B.R. / Arvai, A.S. / Gachhui, R. / Wu, C. / Ghosh, D.K. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A.
History
DepositionJan 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (NITRIC OXIDE SYNTHASE)
B: PROTEIN (NITRIC OXIDE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,67713
Polymers99,4202
Non-polymers2,25711
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-126 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.540, 106.170, 155.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.290062, -0.9358, 0.200355), (-0.940173, -0.317741, -0.122949), (0.178717, -0.152705, -0.971978)
Vector: 2.7318, 23.6065, 97.657)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PROTEIN (NITRIC OXIDE SYNTHASE) / E.C.1.14.13.39 OXIDOREDUCTASE / NOS / ENOS


Mass: 49710.105 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell: ENDOTHELIAL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29473, nitric-oxide synthase (NADPH)

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Non-polymers , 7 types, 486 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-HAR / N-OMEGA-HYDROXY-L-ARGININE


Type: L-peptide linking / Mass: 190.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N4O3
#6: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE / Cacodylic acid


Mass: 137.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7AsO2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Jul 15, 1998 / Details: MIRROR
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 76092 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.053 / Net I/σ(I): 11.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.477 / % possible all: 97.6

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.9→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3328 5 %RANDOM
Rwork0.196 ---
obs0.196 66390 82.9 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6593 0 139 475 7207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.388
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.52
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.265
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.295 314 5 %
Rwork0.279 5865 -
obs--62.4 %

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