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- PDB-5gux: Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 5gux
TitleCytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon
Components
  • (Antibody fab fragment ...) x 2
  • (Nitric oxide reductase subunit ...) x 2
KeywordsMEMBRANE PROTEIN / metal-binding
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
: / HEME C / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / XENON / Nitric oxide reductase subunit C / Nitric oxide reductase subunit B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Pseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
Model detailsnitric oxide reductase and Fab fragment in complex with xenon
AuthorsIshii, S. / Terasaka, E. / Sugimoto, H. / Shiro, Y. / Tosha, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
KAKENHIJP26220807 Japan
KAKENHIJP26620140 Japan
Citation
#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.
#2: Journal: Nat. Struct. Mol. Biol. / Year: 2012
Title: Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus.
Authors: Matsumoto, Y. / Tosha, T. / Pisliakov, A.V. / Hino, T. / Sugimoto, H. / Nagano, S. / Sugita, Y. / Shiro, Y.
#3: 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.
History
DepositionAug 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2017Group: Source and taxonomy / Category: entity_src_nat
Item: _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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

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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)120,29519
Polymers116,4164
Non-polymers3,88015
Water0
1
L: Antibody fab fragment light chain
H: Antibody fab fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)47,8252
Polymers47,8252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-26 kcal/mol
Surface area19450 Å2
MethodPISA
2
B: Nitric oxide reductase subunit B
C: Nitric oxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,47017
Polymers68,5902
Non-polymers3,88015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-143 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.843, 105.379, 192.577
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 / Fragment: Nitric oxide reductase subunit B / Source method: isolated from a natural source / Details: ? / Source: (natural) Pseudomonas aeruginosa PAO1 (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
Fragment: UNP residues 5-146, Nitric oxide reductase subunit C
Mutation: K100N / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (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 / Fragment: antibody fab fragment light chain / 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 / Fragment: antibody fab fragment heavy chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 1 types, 2 molecules

#9: 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, 13 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-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#8: Chemical
ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Xe
#10: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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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: 3.99 Å3/Da / Density % sol: 69.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 24% PEG 400, 0.1M SODIUM CITRATE, 50mM SODIUM CHLORIDE, 20mM MAGNESIUM CHLORIDE

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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: Jun 21, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 27449 / % possible obs: 98.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.131 / Net I/av σ(I): 10.05 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.3-3.364.30.4560.8081100
3.36-3.424.40.4140.88198.6
3.42-3.484.30.4050.867199.9
3.48-3.554.40.3480.859198.5
3.55-3.634.40.30.911198.9
3.63-3.724.50.2950.889199.6
3.72-3.814.50.280.928198.5
3.81-3.914.50.2540.933198.4
3.91-4.034.50.1930.96199.6
4.03-4.164.50.1830.954198.8
4.16-4.314.60.1540.968198.6
4.31-4.484.50.1340.972198.5
4.48-4.684.50.120.981198.4
4.68-4.934.50.1150.978198.4
4.93-5.244.50.1010.985197.8
5.24-5.644.50.0960.987197.9
5.64-6.24.50.0940.985197.5
6.2-7.14.50.0780.991197.7
7.1-8.934.40.0720.993197.1
8.93-404.10.10.981193.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
Coot0.7model building
HKL-2000data reduction
PHASES2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O0R

3o0r


Resolution: 3.3→39.39 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.866 / SU B: 47.351 / SU ML: 0.358 / SU R Cruickshank DPI: 0.4229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.511
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 1369 5 %RANDOM
Rwork0.2092 ---
obs0.2121 26029 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 222.63 Å2 / Biso mean: 88.715 Å2 / Biso min: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.88 Å20 Å20 Å2
2--0.95 Å20 Å2
3---2.93 Å2
Refinement stepCycle: final / Resolution: 3.3→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8060 0 205 0 8265
Biso mean--98.24 --
Num. residues----1029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028529
X-RAY DIFFRACTIONr_angle_refined_deg1.6272.02811632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38851025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73323.204334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68151304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2791536
X-RAY DIFFRACTIONr_chiral_restr0.1030.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216532
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 81 -
Rwork0.27 1620 -
all-1701 -
obs--84.08 %
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)
10.894-0.09620.3880.18510.27090.7332-0.09490.15240.0003-0.03220.1230.0031-0.11640.3418-0.02810.139-0.04150.01170.3072-0.1140.161238.8693-15.5708-0.7705
20.44940.43790.42941.64551.12670.8919-0.08710.11160.0957-0.0685-0.15190.1984-0.0768-0.06030.2390.12390.014-0.02520.2843-0.12440.189117.5216-11.8754-0.0775
30.0764-0.0157-0.12941.46790.95880.83670.08320.0288-0.01690.0148-0.09940.0505-0.1264-0.06390.01620.22120.00240.01080.1115-0.06750.121628.083924.441335.7854
40.4183-1.3584-0.24647.28732.17210.8455-0.0731-0.3094-0.1162-0.49580.30480.0574-0.1353-0.0839-0.23160.4951-0.07180.1450.41090.0730.175320.973615.945356.6198
52.15970.27280.72660.8650.37991.08740.026-0.0046-0.1-0.20690.0292-0.03490.1720.1622-0.05520.15160.0375-0.01490.2213-0.08810.095730.5968-45.0864-21.3925
62.5009-0.4770.5841.24160.1120.20550.0859-0.3469-0.1564-0.1116-0.10040.08110.057-0.11160.01450.17260.01960.01810.2189-0.02320.133820.8948-46.8342-9.8051
70.9265-0.1036-0.070.59521.06151.9363-0.03950.0986-0.10070.16180.02670.03380.22840.10720.01290.2382-0.0048-0.03450.0753-0.07250.186133.9953-3.269528.705
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 DIFFRACTION4C5 - 37
5X-RAY DIFFRACTION5L109 - 213
6X-RAY DIFFRACTION6H125 - 214
7X-RAY DIFFRACTION7C38 - 146

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