[English] 日本語
Yorodumi
- PDB-5obo: Crystal structure of nitrite bound D97N mutant of three-domain he... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5obo
TitleCrystal structure of nitrite bound D97N mutant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii
ComponentsNitrite reductase, copper-containing
KeywordsELECTRON TRANSPORT / nitrite reductase / electron transfer / redox reactions / tyrosine activation
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 / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia sp. 5_2_56FAA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsDong, J. / Sasaki, D. / Eady, R. / Antonyuk, S.V. / Hasnain, S.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L006960/1 United Kingdom
CitationJournal: To be published
Title: Activation of redox tyrosine switch is required for ligand binding at the catalytic site in heme-cu nitrite reductases
Authors: Dong, J. / Sasaki, D. / Eady, R. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionJun 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_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_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.pdbx_dist_value / _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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrite reductase, copper-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9237
Polymers49,9481
Non-polymers9766
Water13,475748
1
A: Nitrite reductase, copper-containing
hetero molecules

A: Nitrite reductase, copper-containing
hetero molecules

A: Nitrite reductase, copper-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,77021
Polymers149,8433
Non-polymers2,92718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area19700 Å2
ΔGint-208 kcal/mol
Surface area44950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.690, 180.690, 180.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-1202-

HOH

21A-1261-

HOH

31A-1285-

HOH

41A-1308-

HOH

51A-1309-

HOH

61A-1322-

HOH

71A-1340-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Nitrite reductase, copper-containing


Mass: 49947.531 Da / Num. of mol.: 1 / Mutation: D97N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia sp. 5_2_56FAA (bacteria) / Gene: HMPREF0989_00586 / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U3G913

-
Non-polymers , 5 types, 754 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 4.36 Å3/Da / Density % sol: 72 % / Description: red cubs
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2M sodium citrate, 20mM Bis-tris-propane-HCl pH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2016 / Details: Mirrors
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.78→90.23 Å / Num. obs: 77285 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.056 / Net I/av σ(I): 8 / Net I/σ(I): 6.7
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 13378 / CC1/2: 0.504 / Rpim(I) all: 0.424 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ziy

3ziy


Resolution: 1.89→90 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.605 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17538 2326 3 %RANDOM
Rwork0.14715 ---
obs0.14796 74954 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.089 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.89→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 60 748 4243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193863
X-RAY DIFFRACTIONr_bond_other_d0.0020.023556
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9865309
X-RAY DIFFRACTIONr_angle_other_deg1.03738324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7245529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63924.671167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5815615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5871518
X-RAY DIFFRACTIONr_chiral_restr0.1020.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214484
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02750
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_it1.7742.5121934
X-RAY DIFFRACTIONr_mcbond_other1.7722.5091933
X-RAY DIFFRACTIONr_mcangle_it2.6653.7542437
X-RAY DIFFRACTIONr_mcangle_other2.6663.7572438
X-RAY DIFFRACTIONr_scbond_it2.5962.761929
X-RAY DIFFRACTIONr_scbond_other2.5792.761927
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9694.042840
X-RAY DIFFRACTIONr_long_range_B_refined9.95234.5984624
X-RAY DIFFRACTIONr_long_range_B_other9.95234.6054625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 160 -
Rwork0.304 5518 -
obs--98.77 %

+
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