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- PDB-1dmi: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 1dmi
TitleBOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH 6S-H4B
ComponentsNITRIC OXIDE SYNTHASE
KeywordsOXIDOREDUCTASE / ALPHA-BETA FOLD
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 / nitric-oxide synthase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / arginine catabolic process / mitochondrion organization / 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 / nitric-oxide synthase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / arginine catabolic process / mitochondrion organization / 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;Heme Domain;Chain A domain 2 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, domain 1 superfamily ...Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase (NOS) signature. / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / 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 reductase-type FAD binding domain profile. / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 6S-5,6,7,8-TETRAHYDROBIOPTERIN / ETHYLISOTHIOUREA / PROTOPORPHYRIN IX CONTAINING FE / CACODYLATE ION / Nitric oxide synthase, endothelial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsRaman, C.S. / Li, H. / Martasek, P. / Kotsonis, P. / Pfleiderer, W. / Schmidt, H.H.H.W. / Masters, B.S.S. / Poulos, T.L.
Citation
Journal: To be Published
Title: Crystal Structures of Bovine Endothelial Nitric Oxide Synthase Heme Domain Complexed with the Pterin Analogues
Authors: Raman, C.S. / Li, H. / Martasek, P. / Kotsonis, P. / Pfleiderer, W. / Schmidt, H.H.H.W. / Southan, G.J. / Masters, B.S.S. / Poulos, T.L.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal Structure of Constitutive Endothelial Nitric Oxide Synthase: 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, A.
History
DepositionDec 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: 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

Downloads & links

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE
B: NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,10417
Polymers99,4202
Non-polymers2,68415
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-114 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.630, 106.560, 156.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NITRIC OXIDE SYNTHASE /


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 / Production host: Escherichia coli (E. coli) / References: UniProt: P29473, nitric-oxide synthase (NADPH)

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Non-polymers , 8 types, 403 molecules

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


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-BHS / 6S-5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3
#7: Chemical ChemComp-ITU / ETHYLISOTHIOUREA


Mass: 104.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8N2S
#8: 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
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsZN ION SITS RIGHT ON THE NCS 2-FOLD THAT DEFINES THE DIMER INTERFACE AND IS COORDINATED ...ZN ION SITS RIGHT ON THE NCS 2-FOLD THAT DEFINES THE DIMER INTERFACE AND IS COORDINATED TETRAHEDRALLY WITH 2 PAIRS OF SYMMETRY-RELATED CYS RESIDUES.

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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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 4000, CACODYLATE, MAGNESIUM ACETATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 63795 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.587 / % possible all: 92.9

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2→32.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2575244.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: RESIDUES 39 TO 66 OF MOLECULE A AND RESIDUES 39 TO 68 IN MOLECULE B ARE NOT VISIBLE IN THE ELECTRON DENSITY. RESIDUES 108-120 ARE DISORDERED, BUT THE TENTATIVE MODEL WAS INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2930 5 %RANDOM
Rwork0.229 ---
obs0.229 58715 87.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.51 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 53.7 Å2
Baniso -1Baniso -2Baniso -3
1-19.09 Å20 Å20 Å2
2---9.16 Å20 Å2
3----9.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6593 0 167 388 7148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.443 282 5.2 %
Rwork0.437 5112 -
obs--81.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3HETEROHETERO.TOP

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