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- PDB-3wfc: Reduced and carbonmonoxide-bound cytochrome c-dependent nitric ox... -

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Basic information

Entry
Database: PDB / ID: 3wfc
TitleReduced and carbonmonoxide-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 / cytochrome-c oxidase activity / 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 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
CARBON MONOXIDE / : / 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: 2.5 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)119,41613
Polymers116,4164
Non-polymers3,0019
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16560 Å2
ΔGint-183 kcal/mol
Surface area39090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.672, 107.072, 196.922
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, 287 molecules

#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#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


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


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.11 Å3/Da / Density % sol: 70.04 %
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: Dec 20, 2012 / Details: mirrors
Diffraction measurementDetails: 0.60 degrees, 10.0 sec, detector distance 199.77 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: 0.079 / Number: 251782
ReflectionResolution: 2.5→50 Å / Num. obs: 65999 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 15.457
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.646 / Rsym value: 0.555 / % possible all: 100
Cell measurementReflection used: 251782

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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: 2.5→33.37 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.612 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.22 / 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 3348 5.1 %RANDOM
Rwork0.1909 ---
obs0.193 65789 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.91 Å2 / Biso mean: 54.9097 Å2 / Biso min: 30.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å2-0 Å2
2---0.59 Å20 Å2
3---2.95 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8060 0 201 280 8541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.028527
X-RAY DIFFRACTIONr_angle_refined_deg1.7832.03611632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42551025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65823.204334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.128151304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0061536
X-RAY DIFFRACTIONr_chiral_restr0.1230.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216460
LS refinement shellResolution: 2.504→2.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 247 -
Rwork0.276 4315 -
all-4562 -
obs--94.16 %
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)
10.9802-0.68210.2721.50280.02750.13670.00550.0640.0473-0.07760.0348-0.08620.00410.1075-0.04030.2269-0.02420.02240.4915-0.07390.284136.1628-15.9503-0.4888
20.69620.41060.51350.95410.54430.9995-0.01630.00570.0901-0.0679-0.02720.0844-0.0115-0.04680.04350.2396-0.0016-0.01340.4481-0.0710.280514.5984-12.2412-0.3278
30.4596-0.5978-0.11111.54891.32481.84810.0021-0.0506-0.0562-0.06320.08620.0099-0.15940.0134-0.08830.3572-0.01060.00690.3571-0.06070.159525.089923.956935.4757
41.9167-4.7484-0.825518.35394.63041.494-0.0521-0.36850.02250.4930.05410.00420.2755-0.0082-0.00190.55180.01740.06130.4228-0.03690.011419.330815.756.9622
52.60670.64011.32560.99811.06861.7343-0.0061-0.01850.0028-0.1580.0081-0.02580.04670.0397-0.00190.2910.0115-0.00590.4022-0.02850.197528.1779-44.9159-22.012
62.0513-0.9368-0.31461.59770.30250.21-0.0653-0.181-0.1863-0.0711-0.03150.06070.0789-0.03860.09680.25230.01540.01360.4355-0.01520.257517.968-47.0447-10.8163
70.2116-0.1847-0.27281.16320.96951.3042-0.07210.0791-0.04630.31220.1199-0.02770.15110.1444-0.04780.30870.0274-0.04450.3928-0.07890.27831.1368-3.618828.266
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 - 807
5X-RAY DIFFRACTION3B808
6X-RAY DIFFRACTION4C5 - 37
7X-RAY DIFFRACTION5L109 - 213
8X-RAY DIFFRACTION6H125 - 214
9X-RAY DIFFRACTION7C38 - 146
10X-RAY DIFFRACTION7C201

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