[English] 日本語
Yorodumi
- PDB-5gux: Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudom... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

-
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

-
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)

-
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

-
Non-polymers , 6 types, 13 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-O / OXYGEN ATOM


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


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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more