[English] 日本語
Yorodumi
- PDB-7s1a: Crystal structure of putative NAD(P)H-flavin oxidoreductase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s1a
TitleCrystal structure of putative NAD(P)H-flavin oxidoreductase from Haemophilus influenzae Rd KW20
ComponentsPutative NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


2,4,6-trinitrotoluene catabolic process / Oxidoreductases / oxidoreductase activity / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FLAVIN MONONUCLEOTIDE / Putative NAD(P)H nitroreductase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMaltseva, N. / Kim, Y. / Endres, M. / Crofts, T. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Microbiol Spectr / Year: 2022
Title: Functional and Structural Characterization of Diverse NfsB Chloramphenicol Reductase Enzymes from Human Pathogens.
Authors: Mullowney, M.W. / Maltseva, N.I. / Endres, M. / Kim, Y. / Joachimiak, A. / Crofts, T.S.
History
DepositionSep 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative NAD(P)H nitroreductase
B: Putative NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7829
Polymers51,6432
Non-polymers1,1397
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-83 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.815, 56.815, 122.924
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

-
Components

#1: Protein Putative NAD(P)H nitroreductase


Mass: 25821.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_1278 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q57431, FMN reductase (NADPH)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 17% PEG10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 31244 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 35.92 Å2 / CC1/2: 0.996 / Net I/σ(I): 20.2
Reflection shellResolution: 1.97→2 Å / Mean I/σ(I) obs: 19 / Num. unique obs: 1475 / CC1/2: 0.394

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KQB

1kqb


Resolution: 1.97→45.68 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.6196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2171 1616 5.18 %
Rwork0.1839 29570 -
obs0.1858 31186 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.93 Å2
Refinement stepCycle: LAST / Resolution: 1.97→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3509 0 73 112 3694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813689
X-RAY DIFFRACTIONf_angle_d0.90264984
X-RAY DIFFRACTIONf_chiral_restr0.0506530
X-RAY DIFFRACTIONf_plane_restr0.0125639
X-RAY DIFFRACTIONf_dihedral_angle_d15.19011416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.29111160.27042395X-RAY DIFFRACTION96.21
2.03-2.090.30151430.24282459X-RAY DIFFRACTION99.66
2.09-2.170.2771200.22162460X-RAY DIFFRACTION100
2.17-2.260.25331140.19552504X-RAY DIFFRACTION100
2.26-2.360.25571460.25812476X-RAY DIFFRACTION100
2.36-2.480.25421200.24582463X-RAY DIFFRACTION100
2.48-2.640.26551100.23322482X-RAY DIFFRACTION99.96
2.64-2.840.25991440.21092521X-RAY DIFFRACTION100
2.84-3.130.27321620.21662413X-RAY DIFFRACTION100
3.13-3.580.22651220.1842504X-RAY DIFFRACTION100
3.58-4.510.17521480.13572464X-RAY DIFFRACTION100
4.51-45.680.16921710.14062429X-RAY DIFFRACTION99.73
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)
13.530085634991.02202479492-1.211470038350.523650876241-1.000309601432.57318677520.3416748128530.040329223420.8142926053080.617098051131-0.07522920392710.236997437604-0.471366443523-0.590999639651-0.4518363297871.265065308890.2172350605850.4354710873780.5252684272350.05414868992840.5891311915632.2370841831453.819501951929.216235388
21.659735807740.396846151355-0.0707007273042.02070644375-1.48887346511.429266043760.2544069875430.3988590882160.6012266943691.028245331810.2410202824280.693476515416-1.26554048645-0.169426771136-0.1638234845160.8197475518740.3676650036190.3354482894240.3107413246450.1834161840470.5924338712887.1411912143662.2781603157.14307044842
31.747822969750.117138573639-0.6406260644493.84941012149-1.775195911953.161229161740.202001900730.4073955086930.199970634393-0.002484058677110.0537914088359-0.0582439953747-0.301738149822-0.088784214859-0.1646665806310.2772986913450.1093621036450.04970344351520.3173654747010.02137072980090.24712906017115.589591478347.68735469363.65468207197
40.485796536424-0.5862817784240.1219166783761.646871405360.03387093827560.1844088126560.2648175131430.03191387090450.3421315864170.7944737537660.5480503022711.18362361271-0.661760050215-0.986977647334-0.3180025650870.7001849771740.3350230609190.4617980811080.5716011028720.272346325810.876446698732-6.223464320348.785144584719.5707651697
51.471671111571.42448105151.44248117795.396581601564.236374614953.3972999570.25179532829-0.4193207962570.1074066953380.5211291385450.617902910951-0.697028147441-0.6493383198230.190407621657-0.3940504712571.49301741531-0.04764581127010.339184747060.470314283987-0.09936866887050.44526433348514.252869580359.820196654725.3306655664
61.16500295714-0.1581784870151.007480597311.78642333164-1.513889256632.786714983450.329010301755-0.0633476240835-0.08218859206160.6957092784060.1256118883910.419111756635-0.672319367554-0.346631102127-0.3290619222290.5107642348060.1451845800030.1436819591810.3661732139940.07764069376170.3324172584866.5153916552542.072382773625.0205366961
72.630485971870.8243073121-0.5970121833254.08301470308-0.5490101614146.50996532327-0.0704500793366-0.23703233899-0.3169537739070.8067083196390.199004691068-0.1052001850740.31924293258-0.0271112523623-0.1570125704640.3640021027220.0361749563133-0.01277445609030.225440250240.02266188226780.290958111919.6335086086530.128478200121.3103592453
82.15747303660.450391948271-0.3274523252652.66419789544-0.9308664561071.843023725010.06191068926990.4310588209820.06890569777780.1130909165070.3392772932610.760471458689-0.0574309729452-0.519710972511-0.2003815292070.2258616192940.06199729900270.02360111818760.4381920192240.1290867259260.400519846631-1.0337544558139.87690142737.66668433087
91.689204086970.705606500597-1.271365422512.23844134147-2.034252870053.010103077470.318291142483-0.0727888354050.1489567108290.652271560277-0.155810434831-0.0884733912575-0.6922580093350.375393009647-0.1450876648460.4497698011250.01158073603150.005324816523480.291926652017-0.03252567216890.25927005854517.947388320748.625669040616.6360956934
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 15 )AA2 - 151 - 14
22chain 'A' and (resid 16 through 81 )AA16 - 8115 - 80
33chain 'A' and (resid 82 through 198 )AA82 - 19881 - 197
44chain 'A' and (resid 199 through 220 )AA199 - 220198 - 219
55chain 'B' and (resid 3 through 15 )BD3 - 151 - 13
66chain 'B' and (resid 16 through 51 )BD16 - 5114 - 49
77chain 'B' and (resid 52 through 89 )BD52 - 8950 - 87
88chain 'B' and (resid 90 through 188 )BD90 - 18888 - 186
99chain 'B' and (resid 189 through 220 )BD189 - 220187 - 218

+
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