[English] 日本語
Yorodumi
- PDB-6qpz: Crystal structure of as isolated Y323E mutant of haem-Cu containi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qpz
TitleCrystal structure of as isolated Y323E 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 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 / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 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 16, 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
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_id / _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_symmetry / _struct_conn_type.id

-
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)101,4129
Polymers99,8292
Non-polymers1,5837
Water20,9871165
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)151,98012
Polymers149,7433
Non-polymers2,2379
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 area17940 Å2
ΔGint-209 kcal/mol
Surface area44170 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)152,25615
Polymers149,7433
Non-polymers2,51312
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 area18730 Å2
ΔGint-211 kcal/mol
Surface area43800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.550, 127.550, 172.680
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-1076-

HOH

21A-1146-

HOH

31A-1153-

HOH

41I-1073-

HOH

51I-1125-

HOH

61I-1151-

HOH

71I-1197-

HOH

81I-1198-

HOH

91I-1203-

HOH

101I-1209-

HOH

-
Components

#1: Protein Copper-containing nitrite reductase


Mass: 49914.457 Da / Num. of mol.: 2 / Mutation: Y323E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: I6NAW4, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2018 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→46.64 Å / Num. obs: 183931 / % possible obs: 98.5 % / Redundancy: 2.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.05 / Net I/σ(I): 8.8
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.167 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.428 / Rpim(I) all: 0.905 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 1.65→42.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.443 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17806 6234 5 %RANDOM
Rwork0.15838 ---
obs0.15937 118437 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.42 Å20 Å2
2--0.83 Å20 Å2
3----2.7 Å2
Refinement stepCycle: 1 / Resolution: 1.65→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6859 0 96 1165 8120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137371
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176776
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.66610084
X-RAY DIFFRACTIONr_angle_other_deg1.451.58415810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3025980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14523.161348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.668151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0921534
X-RAY DIFFRACTIONr_chiral_restr0.0770.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028453
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021491
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_it0.7731.1433714
X-RAY DIFFRACTIONr_mcbond_other0.7731.1423713
X-RAY DIFFRACTIONr_mcangle_it1.2831.7074657
X-RAY DIFFRACTIONr_mcangle_other1.2831.7094658
X-RAY DIFFRACTIONr_scbond_it1.2821.2843657
X-RAY DIFFRACTIONr_scbond_other1.2821.2853655
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0741.875391
X-RAY DIFFRACTIONr_long_range_B_refined5.85116.1368498
X-RAY DIFFRACTIONr_long_range_B_other5.49914.478146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 462 -
Rwork0.371 8772 -
obs--99.34 %
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)
10.0923-0.0850.04890.1884-0.04060.0531-0.0157-0.0145-0.0413-0.0047-0.0260.01540.0028-0.02330.04160.01190.00190.02440.0241-0.0080.3282-10.726-15.957-0.435
20.23460.0307-0.06570.0403-0.01920.03280.00410.00120.04410.0068-0.02170.0207-0.01240.0060.01770.0156-0.0025-0.00160.0133-0.00490.203-8.498-56.367-27.932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 600
2X-RAY DIFFRACTION2I4 - 600

+
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