[English] 日本語
Yorodumi
- PDB-3ek3: Crystal structure of Nitroreductase with Bound FMN (YP_211706.1) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ek3
TitleCrystal structure of Nitroreductase with Bound FMN (YP_211706.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
ComponentsNitroreductase
KeywordsFLAVOPROTEIN / YP_211706.1 / Nitroreductase with Bound FMN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI / OXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 2,4,6-trinitrotoluene catabolic process / nucleotide binding / cytosol
Similarity search - Function
: / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Unknown ligand / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Nitroreductase with Bound FMN (YP_211706.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0896
Polymers21,2791
Non-polymers8115
Water3,693205
1
A: Nitroreductase
hetero molecules

A: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,17912
Polymers42,5572
Non-polymers1,62210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10100 Å2
ΔGint-95 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.610, 83.730, 116.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-394-

HOH

-
Components

#1: Protein Nitroreductase


Mass: 21278.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: YP_211706.1, BF2078 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LDN3
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 65.0000% MPD, 0.1M TRIS pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97932,0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979321
30.979181
ReflectionResolution: 1.7→29.123 Å / Num. obs: 21975 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.497 Å2 / Rmerge F obs: 0.185 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.08 / Net I/σ(I): 10.63 / Num. measured all: 80152
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.761.0890.5211.77757419239590.71594.4
1.76-1.830.8180.3962.27833416640080.54496.2
1.83-1.910.5620.2683.17716408839390.36896.4
1.91-2.020.3790.194.38782466144630.2695.8
2.02-2.140.2670.1366.17458395637860.18795.7
2.14-2.310.1710.098.48257434241940.12396.6
2.31-2.540.1270.06910.97957417440360.09496.7
2.54-2.90.090.0514.58013418840630.06997
2.9-3.660.0450.028238215426841520.03997.3
3.66-29.1230.0270.02131.58164424741230.02997.1

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.123 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.552 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.093
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. 2-METHYL-2,4-PENTANEDIOL MOLECULES FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 5. AN UNKOWN LIGAND (UNL) WAS MODELED INTO THE PUTATIVE IN THE VICINITY OF A BOUND FLAVIN MONONUCLEOTIDE (FMN) COFACTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1124 5.1 %RANDOM
Rwork0.15 20817 --
obs0.152 21941 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 62.52 Å2 / Biso mean: 17.359 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2--2.35 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 63 205 1705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221572
X-RAY DIFFRACTIONr_bond_other_d0.0010.021017
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9942156
X-RAY DIFFRACTIONr_angle_other_deg0.92632496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75624.69766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20215253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.226157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02296
X-RAY DIFFRACTIONr_nbd_refined0.2270.2309
X-RAY DIFFRACTIONr_nbd_other0.1910.21081
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2767
X-RAY DIFFRACTIONr_nbtor_other0.0850.2776
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.223
X-RAY DIFFRACTIONr_mcbond_it1.80331016
X-RAY DIFFRACTIONr_mcbond_other0.4773386
X-RAY DIFFRACTIONr_mcangle_it2.20451534
X-RAY DIFFRACTIONr_scbond_it3.8818734
X-RAY DIFFRACTIONr_scangle_it5.06111615
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 89 -
Rwork0.213 1521 -
all-1610 -
obs--99.2 %
Refinement TLS params.Method: refined / Origin x: 0.5379 Å / Origin y: 27.6876 Å / Origin z: 17.5388 Å
111213212223313233
T0.0405 Å2-0.0051 Å20.0001 Å2-0.0147 Å20.0133 Å2--0.0589 Å2
L0.5338 °2-0.0547 °2-0.0263 °2-0.3766 °20.0972 °2--1.126 °2
S0.0016 Å °0.0987 Å °0.0255 Å °-0.0378 Å °0.0044 Å °0.0429 Å °0.0395 Å °-0.0404 Å °-0.006 Å °

+
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