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- PDB-3wfd: Reduced and acetaldoxime-bound cytochrome c-dependent nitric oxid... -

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Basic information

Entry
Database: PDB / ID: 3wfd
TitleReduced and acetaldoxime-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment
Components
  • (Nitric oxide reductase subunit ...) x 2
  • (antibody fab fragment ...) x 2
KeywordsIMMUNE SYSTEM/OXIDOREDUCTASE / metal-binding / membrane protein / IMMUNE SYSTEM-OXIDOREDUCTASE complex
Function / homology
Function and homology information


nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / denitrification pathway / electron transport coupled proton transport / cytochrome-c oxidase activity / respirasome / aerobic respiration / respiratory electron transport chain / electron transfer activity / heme binding ...nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / denitrification pathway / electron transport coupled proton transport / cytochrome-c oxidase activity / respirasome / aerobic respiration / respiratory electron transport chain / electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c ...Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(1E)-N-hydroxyethanimine / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide reductase subunit C / Nitric oxide reductase subunit B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSato, N. / Ishii, S. / Hino, T. / Sugimoto, H. / Fukumori, Y. / Shiro, Y. / Tosha, T.
Citation
Journal: Proteins / Year: 2014
Title: Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes.
Authors: Sato, N. / Ishii, S. / Sugimoto, H. / Hino, T. / Fukumori, Y. / Sako, Y. / Shiro, Y. / Tosha, T.
#1: Journal: Science / Year: 2010
Title: Structural basis of biological N2O generation by bacterial nitric oxide reductase
Authors: Hino, T. / Matsumoto, Y. / Nagano, S. / Sugimoto, H. / Fukumori, Y. / Murata, T. / Iwata, S. / Shiro, Y.
History
DepositionJul 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: antibody fab fragment light chain
H: antibody fab fragment heavy chain
B: Nitric oxide reductase subunit B
C: Nitric oxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,41912
Polymers116,4164
Non-polymers3,0048
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17030 Å2
ΔGint-179 kcal/mol
Surface area39130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.927, 106.747, 196.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Nitric oxide reductase subunit ... , 2 types, 2 molecules BC

#3: Protein Nitric oxide reductase subunit B / NOR large subunit / Nitric oxide reductase cytochrome b subunit


Mass: 52215.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: PAO1
References: UniProt: Q59647, nitric oxide reductase (cytochrome c)
#4: Protein Nitric oxide reductase subunit C / NOR small subunit / Nitric oxide reductase cytochrome c subunit


Mass: 16374.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / References: UniProt: Q59646

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Antibody , 2 types, 2 molecules LH

#1: Antibody antibody fab fragment light chain


Mass: 23735.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody fab fragment heavy chain


Mass: 24089.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 1 types, 2 molecules

#8: Sugar ChemComp-10M / decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside / (2R,3R,4S,5S,6R)-2-((2R,3S,4R,5R,6S)-6-Decylsulfanyl-4,5-dihydroxy-2-hydroxymethyl-tetrahydro-pyran-3-yloxy)-6-hydroxymethyl-tetrahydro-pyran-3,4,5-triol, n-Decyl-beta-D-thiomaltoside


Type: D-saccharide / Mass: 498.628 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C22H42O10S / Comment: detergent*YM

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Non-polymers , 6 types, 301 molecules

#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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-AXO / (1E)-N-hydroxyethanimine / Acetaldoxime / Acetaldoxime


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 4.09 Å3/Da / Density % sol: 69.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 100mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 7, 2012 / Details: mirrors
Diffraction measurementDetails: 0.60 degrees, 1.9 sec, detector distance 200.00 mm / Method: \w scans
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.096 / Number: 582197
ReflectionResolution: 2.25→50 Å / Num. obs: 83226 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 16.296
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.795 / Rsym value: 0.783 / % possible all: 100
Cell measurementReflection used: 582197

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SPACEdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O0R

3o0r


Resolution: 2.3→33.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.428 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 4224 5.1 %RANDOM
Rwork0.1913 ---
obs0.1933 82815 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.65 Å2 / Biso mean: 60.6795 Å2 / Biso min: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-0 Å20 Å2
2---1.85 Å2-0 Å2
3---3.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8060 0 201 295 8556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.028528
X-RAY DIFFRACTIONr_angle_refined_deg1.9412.03611634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48551025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99623.204334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.435151304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6281536
X-RAY DIFFRACTIONr_chiral_restr0.1460.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0226536
LS refinement shellResolution: 2.296→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 214 -
Rwork0.272 3997 -
all-4211 -
obs--66.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0718-1.030.20651.81460.26530.30420.01290.10.0234-0.11830.0632-0.1104-0.04890.1277-0.07620.1571-0.03420.03030.5135-0.10830.289136.2016-15.8882-0.5099
20.99710.33360.63561.55420.91932.0533-0.03830.02880.1373-0.1181-0.0510.1961-0.1046-0.07930.08930.14550.0044-0.03660.4576-0.09510.274514.6109-12.2056-0.2931
30.4291-0.2912-0.36612.22561.6011.60650.0592-0.06430.0323-0.10180.0819-0.101-0.34290.0892-0.14110.3242-0.04080.00240.3554-0.10430.125925.489624.51935.3825
43.2604-6.797-1.214621.35825.20261.8889-0.0107-0.27540.09020.7433-0.02090.01040.4511-0.00540.03160.5344-0.00980.05120.4054-0.04140.012119.579215.787256.8791
53.35620.84711.63041.50241.26962.3028-0.01720.0049-0.0046-0.24480.0232-0.01240.07210.0882-0.0060.25460.0156-0.01040.3959-0.0450.167528.2174-44.9623-21.8759
61.6436-0.2171-0.46512.66690.69540.3447-0.0487-0.2647-0.193-0.1019-0.0368-0.0070.08520.00750.08540.1960.02790.02780.4459-0.0080.228417.438-48.0386-10.7885
70.98-0.3506-0.51992.38691.17522.3885-0.0593-0.0316-0.0740.42930.1626-0.16720.29030.2653-0.10330.22730.0416-0.07320.3978-0.11810.227731.2893-3.51528.2009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2H1 - 124
3X-RAY DIFFRACTION3B10 - 458
4X-RAY DIFFRACTION3B801 - 804
5X-RAY DIFFRACTION3B806
6X-RAY DIFFRACTION4C5 - 37
7X-RAY DIFFRACTION5L109 - 213
8X-RAY DIFFRACTION6H125 - 225
9X-RAY DIFFRACTION7C38 - 146
10X-RAY DIFFRACTION7C201

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