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- PDB-3wfb: Reduced cytochrome c-dependent nitric oxide reductase (cNOR) from... -

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Basic information

Entry
Database: PDB / ID: 3wfb
TitleReduced 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
: / 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: 2.7 Å
AuthorsSato, N. / Ishii, S. / Hino, T. / Sugimoto, H. / Fukumori, Y. / Shiro, Y. / Tosha, T.
CitationJournal: 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.
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 30, 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)118,39910
Polymers116,4164
Non-polymers1,9836
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16200 Å2
ΔGint-190 kcal/mol
Surface area38790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.763, 110.644, 193.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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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Non-polymers , 6 types, 140 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 134 / 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: 4.17 Å3/Da / Density % sol: 70.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 100 mM 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: Feb 10, 2011 / Details: mirrors
Diffraction measurementDetails: 0.50 degrees, 1.7 sec, detector distance 250.00 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: 0.077 / Number: 216044
ReflectionResolution: 2.7→50 Å / Num. obs: 54416 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 15.966
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.823 / % possible all: 99.5
Cell measurementReflection used: 216044

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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: 2.7→41.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.72 / SU B: 25.378 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.379 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24962 2749 5.1 %RANDOM
Rwork0.20233 ---
obs0.20476 51260 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.461 Å2
Baniso -1Baniso -2Baniso -3
1--7.66 Å20 Å20 Å2
2--3.29 Å2-0 Å2
3---4.37 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8060 0 132 134 8326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.028456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9911542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49451025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04523.204334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.588151304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9691536
X-RAY DIFFRACTIONr_chiral_restr0.120.21249
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216554
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 184 -
Rwork0.329 3677 -
obs--98.39 %
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)
10.7121-0.7862-0.07431.1970.14640.6825-0.04290.16290.0362-0.06280.1744-0.0223-0.1080.141-0.13160.4978-0.06-0.00340.5786-0.15860.493733.8861-16.9909-0.2098
21.50680.51490.91680.98270.97111.210.038-0.10570.2504-0.1786-0.07070.03350.08510.05670.03260.66520.0292-0.04520.5255-0.10030.37125.6073-45.8159-21.9222
30.85780.24080.66721.19390.42580.6237-0.0681-0.06330.1183-0.1353-0.12880.17670.00770.00190.19690.5331-0.0038-0.05820.5872-0.19810.458412.2783-13.36130.3977
41.699-1.2504-0.44721.42610.55790.2443-0.0138-0.3245-0.2242-0.0783-0.16260.25790.0298-0.07090.17650.55960.03860.01450.5839-0.01410.489415.2207-48.8866-10.615
50.50621.53891.05285.88892.42382.80760.3347-0.0982-0.05360.5652-0.2079-0.26450.6431-0.0957-0.12681.1022-0.05930.12520.4272-0.190.131116.653612.069758.5636
60.0328-0.2286-0.14962.11911.36420.9507-0.1045-0.00670.04750.48870.2409-0.15610.20670.0649-0.13640.74290.0579-0.14430.4483-0.23090.504728.9788-5.620429.0364
70.0262-0.0659-0.07341.95121.81771.70420.02780.0619-0.0948-0.0252-0.0392-0.0401-0.0762-0.04280.01140.68270.0429-0.10480.3515-0.2310.386222.749221.833937.7365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 109
2X-RAY DIFFRACTION2L110 - 213
3X-RAY DIFFRACTION3H1 - 124
4X-RAY DIFFRACTION4H125 - 225
5X-RAY DIFFRACTION5C5 - 37
6X-RAY DIFFRACTION6C38 - 146
7X-RAY DIFFRACTION6C201
8X-RAY DIFFRACTION7B10 - 458
9X-RAY DIFFRACTION7B801 - 805

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