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- PDB-1d0c: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 1d0c
TitleBOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH 3-BROMO-7-NITROINDAZOLE (H4B FREE)
ComponentsBOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN
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 / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / mitochondrion organization / nitric oxide biosynthetic process / caveola / FMN binding / flavin adenine dinucleotide binding / NADP binding / calmodulin binding / blood coagulation / 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, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal ...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, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / 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-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 / 3-BROMO-7-NITROINDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase, endothelial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsRaman, C.S. / Li, H. / Martasek, P. / Southan, G.J. / Masters, B.S.S. / Poulos, T.L.
Citation
Journal: Biochemistry / Year: 2001
Title: Crystal structure of nitric oxide synthase bound to nitro indazole reveals a novel inactivation mechanism.
Authors: Raman, C.S. / Li, H. / Martasek, P. / Southan, G. / Masters, B.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. / 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 Complexes
Authors: Crane, B.R. / Arvai, A.S. / Gachhui, R. / Wu, C. / Ghosh, D.K. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A.
History
DepositionSep 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: 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: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN
B: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,38317
Polymers99,4202
Non-polymers2,96315
Water11,800655
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12220 Å2
ΔGint-111 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.44, 105.98, 155.79
Angle α, β, γ (deg.)90, 90, 90
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 BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN


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

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Non-polymers , 7 types, 670 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-ZN / ZINC ION / Zinc


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-INE / 3-BROMO-7-NITROINDAZOLE


Mass: 242.030 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H4BrN3O2
#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.: 655 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 4000, CACODYLATE, MAGNESSIUM ACETATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280.0K
Crystal grow
*PLUS
Details: Raman, C.S., (1998) Cell (Cambridge,Mass.), 95, 939.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %PEG33501reservoir
2200 mMmagnesium acetate1reservoir
3100 mMsodium cacodylate1reservoir
41 mMSEITU1dropcan be replaced by 5mM L-Arg
50.035 mMSDS1drop
65 mMTCEP1dropcan be replaced by 5mM glutathione sulfonate

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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: Aug 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 116411 / Num. obs: 114549 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3 % / Rmerge(I) obs: 0.586 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 398353
Reflection shell
*PLUS
% possible obs: 99.1 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.65→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.259 5422 5 %RANDOM
Rwork0.213 ---
all-112609 --
obs-107187 99 %-
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6593 0 173 655 7421
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS

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