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- PDB-2fbz: Heme-No complex in a bacterial Nitric Oxide Synthase -

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Basic information

Entry
Database: PDB / ID: 2fbz
TitleHeme-No complex in a bacterial Nitric Oxide Synthase
ComponentsNitric oxide synthase oxygenase
KeywordsOXIDOREDUCTASE / Heme-NO complex / Nitric Oxide Synthase
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, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 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, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-H2B / N-OMEGA-HYDROXY-L-ARGININE / PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Nitric oxide synthase oxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPant, K. / Crane, B.R.
CitationJournal: Biochemistry / Year: 2006
Title: Nitrosyl-heme structures of Bacillus subtilis nitric oxide synthase have implications for understanding substrate oxidation.
Authors: Pant, K. / Crane, B.R.
History
DepositionDec 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE RESIDUES GLU 133 AND GLY 136 ARE LINKED TOGETHER. AUTHOR STATES THAT THERE WAS NO ...SEQUENCE RESIDUES GLU 133 AND GLY 136 ARE LINKED TOGETHER. AUTHOR STATES THAT THERE WAS NO COVALENT/PEPTIDE BOND AND ELECTRON DENSITY BETWEEN THESE RESIDUES.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
X: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1735
Polymers42,0971
Non-polymers1,0764
Water5,368298
1
X: Nitric oxide synthase oxygenase
hetero molecules

X: Nitric oxide synthase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,34610
Polymers84,1942
Non-polymers2,1528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)79.995, 93.503, 62.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Nitric oxide synthase oxygenase / NOSoxy-like protein


Mass: 42097.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: nos / Production host: Escherichia coli (E. coli) / References: UniProt: O34453

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Non-polymers , 5 types, 302 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-H2B / 2-AMINO-6-(1,2-DIHYDROXY-PROPYL)-7,8-DIHYDRO-6H-PTERIDIN-4-ONE / QUINONOID 7,8-TETRAHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O3
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 5-10% PEG8K, NOC-12, Potassium Acetate, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.93
SYNCHROTRONCHESS F120.92
SYNCHROTRONCHESS F130.92
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.931
20.921
ReflectionResolution: 1.9→30 Å / Num. all: 36005 / Num. obs: 35595 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 1.9 Å / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.401 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1275 4.8 %RANDOM
Rwork0.23144 ---
obs0.23235 25095 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.754 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å20 Å2
2---1.39 Å20 Å2
3---4.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 75 298 3306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213092
X-RAY DIFFRACTIONr_angle_refined_deg2.1361.984208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.5425358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47123.831154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51515510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9691522
X-RAY DIFFRACTIONr_chiral_restr0.1840.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022390
X-RAY DIFFRACTIONr_nbd_refined0.2940.21749
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.2257
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5080.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7060.29
X-RAY DIFFRACTIONr_mcbond_it1.8121.51864
X-RAY DIFFRACTIONr_mcangle_it2.65522900
X-RAY DIFFRACTIONr_scbond_it4.15231455
X-RAY DIFFRACTIONr_scangle_it6.1324.51299
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 107 -
Rwork0.305 1880 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 6.4561 Å / Origin y: 28.1697 Å / Origin z: 7.0967 Å
111213212223313233
T0.1022 Å20.0274 Å20.002 Å2-0.0849 Å2-0.0425 Å2---0.0374 Å2
L0.8072 °2-0.1331 °20.1575 °2-1.1327 °2-0.3899 °2--0.3918 °2
S-0.0181 Å °-0.0575 Å °-0.1237 Å °0.0257 Å °-0.0223 Å °-0.1004 Å °0.0842 Å °0.0635 Å °0.0404 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA-3 - 3591 - 363
2X-RAY DIFFRACTION1XB901
3X-RAY DIFFRACTION1XC903
4X-RAY DIFFRACTION1XE909
5X-RAY DIFFRACTION1XF910 - 1210

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