[English] 日本語
Yorodumi
- PDB-6qpx: Crystal structure of nitrite bound Y323A mutant of haem-Cu contai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qpx
TitleCrystal structure of nitrite bound Y323A mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii
ComponentsCopper-containing nitrite reductase
KeywordsMETAL BINDING PROTEIN / haem and Cu containing nitrite reductase / inter-copper electron transfer
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding
Similarity search - Function
Cytochrome C oxidase, cbb3-type, subunit III / Nitrite reductase, copper-type / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain ...Cytochrome C oxidase, cbb3-type, subunit III / Nitrite reductase, copper-type / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / HEME C / NITRITE ION / Copper-containing nitrite reductase / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsAntonyuk, S.V. / Shenoy, R.T. / Hedison, T.M. / Eady, R.R. / Hasnain, S.S. / Scrutton, N.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N019380/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N013972/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2019
Title: Unexpected Roles of a Tether Harboring a Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis.
Authors: Hedison, T.M. / Shenoy, R.T. / Iorgu, A.I. / Heyes, D.J. / Fisher, K. / Wright, G.S.A. / Hay, S. / Eady, R.R. / Antonyuk, S.V. / Hasnain, S.S. / Scrutton, N.S.
History
DepositionFeb 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Copper-containing nitrite reductase
I: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,29610
Polymers99,7132
Non-polymers1,5838
Water21,1501174
1
A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,94415
Polymers149,5693
Non-polymers2,37512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area18440 Å2
ΔGint-205 kcal/mol
Surface area44590 Å2
MethodPISA
2
I: Copper-containing nitrite reductase
hetero molecules

I: Copper-containing nitrite reductase
hetero molecules

I: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,94415
Polymers149,5693
Non-polymers2,37512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area18440 Å2
ΔGint-206 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.500, 128.500, 172.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1159-

HOH

21A-1161-

HOH

31A-1166-

HOH

41A-1167-

HOH

51A-1173-

HOH

61A-1176-

HOH

71I-1045-

HOH

81I-1089-

HOH

91I-1140-

HOH

101I-1182-

HOH

111I-1185-

HOH

121I-1189-

HOH

131I-1196-

HOH

-
Components

#1: Protein Copper-containing nitrite reductase


Mass: 49856.422 Da / Num. of mol.: 2 / Mutation: Y323A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: NCIMB 13142 / Gene: HMPREF0989_00586 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli)
References: UniProt: U3G913, UniProt: I6NAW4*PLUS, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1174 / 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: 2.74 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2018
RadiationMonochromator: si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.61→30.1 Å / Num. obs: 137234 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 14.878 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.071 / Net I/av σ(I): 7.6 / Net I/σ(I): 0.997
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 5 % / Rmerge(I) obs: 1.8 / Num. unique obs: 6817 / CC1/2: 0.448 / Rpim(I) all: 0.89 / Χ2: 1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 1.7→29.33 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.972 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20303 5447 4.7 %RANDOM
Rwork0.1738 ---
obs0.17518 111132 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å20 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.7→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6839 0 96 1174 8109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137287
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176673
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6669971
X-RAY DIFFRACTIONr_angle_other_deg1.3631.58315561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2665960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05723.255341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.037151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5661532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028365
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021471
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_it0.741.4043694
X-RAY DIFFRACTIONr_mcbond_other0.7371.4023693
X-RAY DIFFRACTIONr_mcangle_it1.2282.0994630
X-RAY DIFFRACTIONr_mcangle_other1.2282.14631
X-RAY DIFFRACTIONr_scbond_it1.131.5323593
X-RAY DIFFRACTIONr_scbond_other1.1291.5313589
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8382.2355315
X-RAY DIFFRACTIONr_long_range_B_refined5.9819.2638395
X-RAY DIFFRACTIONr_long_range_B_other5.46117.4548003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 418 -
Rwork0.373 8260 -
obs--99.98 %
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)
10.7083-0.38350.2780.6671-0.2820.47640.001-0.0146-0.0947-0.0168-0.02040.0380.0633-0.04910.01940.0188-0.01620.01370.0185-0.00960.0235-10.782-16.063-0.595
20.97380.2139-0.38710.3392-0.0980.39120.01330.02010.08690.0093-0.01510.0638-0.0477-0.02730.00170.02420.0058-0.00820.0038-0.0050.0216-8.588-56.819-27.825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 701
2X-RAY DIFFRACTION2I5 - 701

+
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