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- PDB-3wfe: Reduced and cyanide-bound cytochrome c-dependent nitric oxide red... -

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Basic information

Entry
Database: PDB / ID: 3wfe
TitleReduced and cyanide-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
CYANIDE ION / : / 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: 2.49 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)119,41213
Polymers116,4164
Non-polymers2,9979
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16940 Å2
ΔGint-179 kcal/mol
Surface area38690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.688, 107.381, 195.288
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, 249 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-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#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.: 242 / 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: 4.08 Å3/Da / Density % sol: 69.88 %
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: Jan 24, 2012 / Details: mirrors
Diffraction measurementDetails: 0.60 degrees, 1.8 sec, detector distance 220.00 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: 0.076 / Number: 492828
ReflectionResolution: 2.49→50 Å / Num. obs: 66399 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 24.231
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3.684 / Rsym value: 0.526 / % possible all: 100
Cell measurementReflection used: 492828

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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: 2.49→35.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.756 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 3358 5.1 %RANDOM
Rwork0.1888 ---
obs0.1907 66111 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 170.95 Å2 / Biso mean: 61.6746 Å2 / Biso min: 33.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0 Å2
2---0.7 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.49→35.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8060 0 201 242 8503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.028527
X-RAY DIFFRACTIONr_bond_other_d0.0020.027955
X-RAY DIFFRACTIONr_angle_refined_deg1.8082.03611632
X-RAY DIFFRACTIONr_angle_other_deg0.983.02318133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64651025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47623.204334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.202151304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6121536
X-RAY DIFFRACTIONr_chiral_restr0.1120.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0229644
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022020
LS refinement shellResolution: 2.494→2.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 222 -
Rwork0.25 4392 -
all-4614 -
obs--94.28 %
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)
10.9292-0.73170.17241.1308-0.0390.0603-0.05690.11820.0136-0.03430.1023-0.0447-0.03050.1131-0.04530.2223-0.0370.02780.4339-0.11730.255536.1344-16.227-0.5563
20.79760.35530.45830.66460.79361.0111-0.05660.00640.0955-0.0782-0.02820.0873-0.0375-0.05130.08480.2498-0.0045-0.03110.3811-0.09120.266814.4466-12.5445-0.6053
30.1975-0.3597-0.34311.82711.44711.21780.0477-0.0486-0.0362-0.17310.0372-0.0611-0.26080.0725-0.08490.4353-0.03150.03210.2704-0.09360.152925.163724.282235.016
41.321-3.7948-0.594515.28243.99061.5164-0.0481-0.1390.11230.9475-0.0623-0.01510.4603-0.03810.11030.57760.00550.07990.3851-0.02260.033519.15216.254256.6246
52.66960.62240.90580.60070.92921.5703-0.0266-0.03650.0413-0.13590.03190.0082-0.00480.0705-0.00530.36830.0197-0.03190.3264-0.05760.199528.1782-45.0608-21.9802
61.9648-0.9806-0.56911.45480.20390.3394-0.0463-0.2046-0.1674-0.0535-0.06160.12140.0681-0.00940.10790.23760.0137-0.00350.3799-0.03980.258617.2684-48.0988-10.7864
70.3248-0.4788-0.73371.69391.41921.8238-0.11040.02680.02330.38710.2077-0.01440.26070.1416-0.09730.32640.035-0.07450.3535-0.12250.257531.2456-3.748128.2846
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 - 806
5X-RAY DIFFRACTION3C201
6X-RAY DIFFRACTION3B807
7X-RAY DIFFRACTION4C5 - 37
8X-RAY DIFFRACTION5L109 - 213
9X-RAY DIFFRACTION6H125 - 225
10X-RAY DIFFRACTION7C38 - 146

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