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- PDB-1m7z: Structure of Nitric Oxide Synthase Heme Protein from Bacillus Sub... -

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Basic information

Entry
Database: PDB / ID: 1m7z
TitleStructure of Nitric Oxide Synthase Heme Protein from Bacillus Subtilis with N-Hydroxy-Arginine and Tetrahydrofolate Bound
ComponentsNitric oxide synthase
KeywordsOXIDOREDUCTASE / oxygenase / tetrahydrofolate / pterin / bacteria / heme / hydroxy arginine
Function / homology
Function and homology information


nitric-oxide synthase (flavodoxin) / nitric-oxide synthase activity / nitric oxide biosynthetic process / heme binding / metal ion binding
Similarity search - Function
Nitric oxide synthase, oxygenase subunit / 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;Heme Domain;Chain A domain 2 / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily ...Nitric oxide synthase, oxygenase subunit / 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;Heme Domain;Chain A domain 2 / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
N-OMEGA-HYDROXY-L-ARGININE / PROTOPORPHYRIN IX CONTAINING FE / (6S)-5,6,7,8-TETRAHYDROFOLATE / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsPant, K. / Bilwes, A.M. / Adak, S. / Stuehr, D.J. / Crane, B.R.
CitationJournal: Biochemistry / Year: 2002
Title: Structure of a nitric oxide synthase heme protein from Bacillus subtilis.
Authors: Pant, K. / Bilwes, A.M. / Adak, S. / Stuehr, D.J. / Crane, B.R.
History
DepositionJul 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE At the time of processing, this sequence of chain A has not yet been deposited in a ...SEQUENCE At the time of processing, this sequence of chain A has not yet been deposited in a sequence database. Author also states that there was no covalent/peptide bond and electron density between residues 133 and 136.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1474
Polymers41,8951
Non-polymers1,2523
Water3,675204
1
A: Nitric oxide synthase
hetero molecules

A: Nitric oxide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2948
Polymers83,7902
Non-polymers2,5046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)81.085, 93.068, 62.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1202-

HOH

DetailsThe second half of the biological dimer is generated by rotation about the crystallographic two-fold axis -x, -y, Z

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Components

#1: Protein Nitric oxide synthase / Nitric-oxide synthetase / NO synthase / Endothelium-derived relaxation factor-forming enzyme / ...Nitric-oxide synthetase / NO synthase / Endothelium-derived relaxation factor-forming enzyme / Endothelium-derived relaxingfactor synthase


Mass: 41895.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pet15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 (DE3) / References: UniProt: O34453, nitric-oxide synthase (NADPH)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-HAR / N-OMEGA-HYDROXY-L-ARGININE


Type: L-peptide linking / Mass: 190.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N4O3
#4: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: PEG 8K, potassium acetate, pH 7.0, VAPOR DIFFUSION, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
145 mg/mlprotein1drop
233 mMTHF1drop
350 mMTris1droppH7.5
4150 mM1dropNaCl
52 mMdithiothreitol1drop
6100 mMsodium cacodylate1reservoirpH6.0-6.8
7200 mMpotassium acetate1reservoir
816-21 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 25, 2002
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.14→30 Å / Num. all: 37880 / Num. obs: 37880 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 33.4 Å2 / Rsym value: 0.086 / Net I/σ(I): 10.1
Reflection shellResolution: 2.14→2.2 Å / Mean I/σ(I) obs: 8.6 / Rsym value: 0.467 / % possible all: 99.2
Reflection
*PLUS
Highest resolution: 2.13 Å / Num. measured all: 199903 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 2.13 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DWW

1dww


Resolution: 2.14→29.74 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1428377.04 / Data cutoff high rms absF: 1428377.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The glutamate moiety of tetrahydrofolate is not well ordered and likely has alternate conformations
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1276 4.8 %RANDOM
Rwork0.212 ---
all-37880 --
obs-37880 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.3727 Å2 / ksol: 0.339097 e/Å3
Displacement parametersBiso mean: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1--14.82 Å20 Å20 Å2
2---4.95 Å20 Å2
3---19.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.14→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 88 204 3225
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.55
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.14→2.27 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 189 4.7 %
Rwork0.321 3846 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMEWATER.TOP
X-RAY DIFFRACTION3WATER.PARAMTOPH19X.HEME
X-RAY DIFFRACTION4THF-8.PARAMTHF-6.TOP
Refinement
*PLUS
Highest resolution: 2.13 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.55
LS refinement shell
*PLUS
Highest resolution: 2.13 Å / Lowest resolution: 2.2 Å / Rfactor Rfree: 0.355 / Rfactor Rwork: 0.321

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