[English] 日本語
Yorodumi
- PDB-3wfc: Reduced and carbonmonoxide-bound cytochrome c-dependent nitric ox... -

+
Open data


ID or keywords:

Loading...

-
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 / : / electron transport coupled proton transport / aerobic respiration / respiratory electron transport chain / electron transfer activity / heme binding ...nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / denitrification pathway / cytochrome-c oxidase activity / : / electron transport coupled proton transport / 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
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

-
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)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

-
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 / 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

-
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)

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://pdbjlvh1.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