[English] 日本語
Yorodumi
- PDB-5tb7: Structure of nitrite reductase AniA from Neisseria gonorrhoeae, s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tb7
TitleStructure of nitrite reductase AniA from Neisseria gonorrhoeae, space group P212121
ComponentsNitrite reductase
KeywordsOXIDOREDUCTASE / NGO1276
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / cell outer membrane / periplasmic space / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / PHOSPHATE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsHamza, A. / Williamson, Z.A. / Reed, R.W. / Sikora, A.E. / Korotkov, K.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI117235 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Peptide Inhibitors Targeting the Neisseria gonorrhoeae Pivotal Anaerobic Respiration Factor AniA.
Authors: Sikora, A.E. / Mills, R.H. / Weber, J.V. / Hamza, A. / Passow, B.W. / Romaine, A. / Williamson, Z.A. / Reed, R.W. / Zielke, R.A. / Korotkov, K.V.
History
DepositionSep 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 9, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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
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.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrite reductase
B: Nitrite reductase
C: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,86012
Polymers109,1943
Non-polymers6669
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-94 kcal/mol
Surface area30410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.230, 129.100, 136.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Nitrite reductase


Mass: 36397.992 Da / Num. of mol.: 3 / Fragment: Residues 42-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: NGO_1276 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5F7A4
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS-HCL pH 8.5, 2.0M ammonium dihydrogen phosphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 23, 2015
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→66.58 Å / Num. obs: 105957 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 37.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
1.9-1.956.31.0381.860.677100
1.95-20.7472.590.78799.9
2-2.060.5853.290.851100
2.06-2.120.4754.050.896100
2.12-2.190.3765.020.932100
2.19-2.270.3135.970.95100
2.27-2.360.2577.10.96599.9
2.36-2.450.2168.250.97399.9
2.45-2.560.1789.670.98399.8
2.56-2.690.14911.250.98799.8
2.69-2.830.12313.260.9999.4
2.83-30.09216.650.99599.7
3-3.210.07919.130.99599.1
3.21-3.470.063230.99698.4
3.47-3.80.05825.560.99698.2
3.8-4.250.05227.80.99797.6
4.25-4.910.0529.450.99796.4
4.91-6.010.04929.760.99796.4
6.01-8.50.04630.030.99794.9
8.50.04830.060.99793.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.99 Å66.58 Å
Translation7.99 Å66.58 Å

-
Processing

Software
NameVersionClassification
XSCALENovember 3, 2014 BUILT=20141118data scaling
PHASER2.5.7phasing
PHENIXdev_2481refinement
PDB_EXTRACT3.2data extraction
XDSNovember 3, 2014data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KBV

1kbv


Resolution: 1.9→66.58 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 18.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.179 10240 5.08 %Random selection
Rwork0.1554 ---
obs0.1566 105946 98.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.26 Å2 / Biso mean: 38.0451 Å2 / Biso min: 19.09 Å2
Refinement stepCycle: final / Resolution: 1.9→66.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7111 0 21 486 7618
Biso mean--53.74 41.85 -
Num. residues----934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017345
X-RAY DIFFRACTIONf_angle_d1.0069983
X-RAY DIFFRACTIONf_chiral_restr0.0681086
X-RAY DIFFRACTIONf_plane_restr0.0071324
X-RAY DIFFRACTIONf_dihedral_angle_d11.2994366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.34343450.310764816826100
1.9216-1.94420.28843400.287464496789100
1.9442-1.96790.30513320.264765126844100
1.9679-1.99280.27343650.24764556820100
1.9928-2.01910.27813140.239365166830100
2.0191-2.04670.27053580.231164966854100
2.0467-2.0760.23273140.226164936807100
2.076-2.1070.24483930.212564706863100
2.107-2.13990.22553770.203264146791100
2.1399-2.1750.21843580.189665146872100
2.175-2.21250.2193540.189664516805100
2.2125-2.25270.19913470.179864326779100
2.2527-2.2960.20923860.17786458684499
2.296-2.34290.2083590.167164456804100
2.3429-2.39380.21263460.1676427677399
2.3938-2.44950.18233200.16126509682999
2.4495-2.51080.17073250.15236430675599
2.5108-2.57870.18893950.14886394678999
2.5787-2.65460.19123160.14596433674999
2.6546-2.74030.18053150.14746454676998
2.7403-2.83820.17272790.1456421670098
2.8382-2.95180.15742890.13796420670998
2.9518-3.08620.15453030.14086347665097
3.0862-3.24890.16183870.14596274666197
3.2489-3.45240.15633600.13646163652395
3.4524-3.7190.16823230.12936177650095
3.719-4.09320.13723640.12016111647594
4.0932-4.68530.12032870.10956076636393
4.6853-5.90250.14933340.12346057639193
5.9025-66.62110.19233550.18615974632993

+
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