[English] 日本語
Yorodumi
- PDB-2wzv: Crystal structure of the FMN-dependent nitroreductase NfnB from M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wzv
TitleCrystal structure of the FMN-dependent nitroreductase NfnB from Mycobacterium smegmatis
ComponentsNFNB PROTEIN
KeywordsOXIDOREDUCTASE / NITROREDUCTASE
Function / homology
Function and homology information


Oxidoreductases / xenobiotic catabolic process / FMN binding / NADP binding / oxidoreductase activity / protein homodimerization activity / identical protein binding
Similarity search - Function
: / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Nitroreductase NfnB
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsBellinzoni, M. / Manina, G. / Riccardi, G. / Alzari, P.M.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Biological and Structural Characterization of the Mycobacterium Smegmatis Nitroreductase Nfnb, and its Role in Benzothiazinone Resistance
Authors: Manina, G. / Bellinzoni, M. / Pasca, M.R. / Neres, J. / Milano, A. / Ribeiro, A.L. / Buroni, S. / Skovierova, H. / Dianiskova, P. / Mikusova, K. / Marak, J. / Makarov, V. / Giganti, D. / ...Authors: Manina, G. / Bellinzoni, M. / Pasca, M.R. / Neres, J. / Milano, A. / Ribeiro, A.L. / Buroni, S. / Skovierova, H. / Dianiskova, P. / Mikusova, K. / Marak, J. / Makarov, V. / Giganti, D. / Haouz, A. / Lucarelli, A.P. / Degiacomi, G. / Piazza, A. / Chiarelli, L.R. / De Rossi, E. / Salina, E. / Cole, S.T. / Alzari, P.M. / Riccardi, G.
History
DepositionDec 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NFNB PROTEIN
B: NFNB PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,35210
Polymers51,8782
Non-polymers1,4748
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-76.8 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.190, 114.971, 118.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-2160-

HOH

21B-2169-

HOH

-
Components

#1: Protein NFNB PROTEIN / NITROREDUCTASE NFNB


Mass: 25939.205 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0R6D0
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST GLY RESIDUE IS A PURIFICATION TAG LEFTOVER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 8
Details: 20% (W/V) PEG8000, 6% (V/V) ISOPROPANOL, 200 MM NH4H2PO4, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0332
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 26, 2009 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→44.2 Å / Num. obs: 58860 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
SHELX-AUTOSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.75→35 Å / Cor.coef. Fo:Fc: 0.9578 / Cor.coef. Fo:Fc free: 0.9535 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.079
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAIN ISOTROPIC EQUIVALENTS OF THE SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 2989 5.08 %RANDOM
Rwork0.1507 ---
obs0.1519 58852 99.66 %-
Displacement parametersBiso mean: 23.67 Å2
Baniso -1Baniso -2Baniso -3
1-3.9118 Å20 Å20 Å2
2---1.7364 Å20 Å2
3----2.1755 Å2
Refine analyzeLuzzati coordinate error obs: 0.161 Å
Refinement stepCycle: LAST / Resolution: 1.75→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 95 359 3867
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013649HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.924973HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1259SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes563HARMONIC5
X-RAY DIFFRACTIONt_it3583HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion15.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion464SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4597SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2354 211 4.91 %
Rwork0.1891 4083 -
all0.1914 4294 -
obs--99.66 %
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)
11.076-0.1234-0.01370.5981-0.05280.4511-0.00890.16360.2221-0.0513-0.0130.0297-0.0582-0.02040.02190.03620.0027-0.0050.07230.0260.0574-26.9862-84.4231-29.3348
22.9445-0.60560.3980.67720.47441.543-0.1205-0.0150.50390.1401-0.1152-0.0082-0.20930.08540.23570.009-0.0333-0.0358-0.0019-0.02140.1759-10.4161-74.59-19.1032
35.434411.4670.611810.10781.14410.62590.0864-0.91061.02120.2641-0.50260.2355-0.1585-0.0360.41620.142-0.0018-0.07620.2109-0.06260.5085-18.1092-62.8072-25.8853
41.1978-0.27480.31390.5469-0.23060.4272-0.0190.0830.1688-0.0047-0.0055-0.0118-0.02250.01230.02450.0511-0.00360.00530.06680.010.0833-22.9755-84.0818-24.5477
50.547-0.36190.04170.82640.03510.4317-0.02630.0254-0.03550.05620.0063-0.07160.08670.05230.020.06590.0050.01120.0841-0.0070.071-12.1577-102.464-18.7769
60-0.24374.55813.081-25.407546.81110.03550.0641-0.0782-0.20170.27620.19490.2799-1.3089-0.31170.21560.0950.03190.75940.06530.2819-32.7184-94.634-5.4962
71.12620.35840.09712.5204-1.69742.8834-0.0465-0.1168-0.08360.29070.12870.44890.0325-0.1992-0.08210.0818-0.04230.06570.13630.01650.0836-32.32-111.764-11.7216
80.6662-0.2917-0.08680.751-0.09170.2681-0.01360.01150.01240.03640.00950.00510.04060.01790.00410.0528-0.00150.00150.0505-0.01380.0346-17.9793-101.15-16.7038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 13:91)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 92:119)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 120:132)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 133:234)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 12:91)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 92:98)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 99:127)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 128:234)

+
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