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- PDB-1m7v: STRUCTURE OF A NITRIC OXIDE SYNTHASE HEME PROTEIN FROM BACILLUS S... -

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Basic information

Entry
Database: PDB / ID: 1m7v
TitleSTRUCTURE OF A NITRIC OXIDE SYNTHASE HEME PROTEIN FROM BACILLUS SUBTILIS WITH TETRAHYDROFOLATE AND ARGININE BOUND
ComponentsNitric Oxide Synthase
KeywordsOXIDOREDUCTASE / pterin oxygenase / bacteria / nitric oxide / heme
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
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: 1.95 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 22, 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 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_initial_refinement_model / struct_conn / struct_conn_type / 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.

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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)43,3344
Polymers42,0971
Non-polymers1,2373
Water4,648258
1
A: Nitric Oxide Synthase
hetero molecules

A: Nitric Oxide Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6698
Polymers84,1942
Non-polymers2,4746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)81.155, 92.553, 62.939
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-2329-

HOH

DetailsThe second half of the biologically active dimer is generated by the crystallographic two fold axis: -x, -y, z

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Components

#1: Protein Nitric Oxide Synthase


Mass: 42097.227 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-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 258 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56.17 %
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 24, 2002
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. all: 44343 / Num. obs: 44343 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.059 / Net I/σ(I): 27.5
Reflection shellResolution: 1.94→1.98 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.399 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 395408 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.399

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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: 1.95→29.8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1406462.31 / Data cutoff high rms absF: 1406462.31 / 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 1748 5 %RANDOM
Rwork0.225 ---
all-44343 --
obs-44343 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.1565 Å2 / ksol: 0.338359 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--12.57 Å20 Å20 Å2
2--0.21 Å20 Å2
3---12.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.95→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 87 258 3278
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.55
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it1.412
X-RAY DIFFRACTIONc_scangle_it2.22.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 276 4.8 %
Rwork0.322 5496 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4THF-8.PARAMTHF-6.TOP
X-RAY DIFFRACTION5ARG.PARAMARG.TOP
Refinement
*PLUS
Highest resolution: 1.94 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.55
LS refinement shell
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 1.98 Å / Rfactor Rfree: 0.333 / Rfactor Rwork: 0.322

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