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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ldq
TitleCrystal structure of putative NAD(P)H-flavin oxidoreductase from Haemophilus influenzae R2846
ComponentsNAD(P)H-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyOxygen-insensitive NAD(P)H nitroreductase NfsB-like / Nitroreductase / Nitroreductase family / Nitroreductase-like / oxidoreductase activity / ACETIC ACID / FLAVIN MONONUCLEOTIDE / FORMIC ACID / NAD(P)H-dependent oxidoreductase
Function and homology information
Biological speciesHaemophilus influenzae R2846 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 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: To Be Published
Title: Crystal structure of putative NAD(P)H-flavin oxidoreductase from Haemophilus influenzae R2846
Authors: Maltseva, N. / Kim, Y. / Endres, M. / Crofts, T. / Joachimiak, A.
History
DepositionJan 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD(P)H-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6307
Polymers25,9461
Non-polymers6846
Water3,369187
1
A: NAD(P)H-dependent oxidoreductase
hetero molecules

A: NAD(P)H-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,26114
Polymers51,8932
Non-polymers1,36812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11600 Å2
ΔGint-87 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.100, 84.838, 53.977
Angle α, β, γ (deg.)90.000, 115.831, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-412-

HOH

31A-429-

HOH

41A-441-

HOH

51A-494-

HOH

61A-548-

HOH

71A-549-

HOH

81A-574-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein NAD(P)H-dependent oxidoreductase / flavin reductase


Mass: 25946.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae R2846 (bacteria)
Gene: CH638_05260 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A3E1QXW7, Oxidoreductases

-
Non-polymers , 6 types, 193 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate, pH 6.5, 40% PEG300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 6, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 74481 / % possible obs: 98 % / Redundancy: 4.6 % / Biso Wilson estimate: 12.91 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 18.8
Reflection shellResolution: 1.15→1.17 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3643 / CC1/2: 0.811

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→31.95 Å / SU ML: 0.0919 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 13.0371
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1588 3664 4.92 %
Rwork0.1424 70808 -
obs0.1432 74472 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.23 Å2
Refinement stepCycle: LAST / Resolution: 1.15→31.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 43 187 2005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542188
X-RAY DIFFRACTIONf_angle_d0.80122983
X-RAY DIFFRACTIONf_chiral_restr0.0765302
X-RAY DIFFRACTIONf_plane_restr0.0073401
X-RAY DIFFRACTIONf_dihedral_angle_d21.766871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.170.19171670.17632541X-RAY DIFFRACTION93.41
1.17-1.180.15981250.16932695X-RAY DIFFRACTION96.51
1.18-1.20.19191310.15292716X-RAY DIFFRACTION97.23
1.2-1.220.17841340.14772725X-RAY DIFFRACTION97.38
1.22-1.240.16781400.1392677X-RAY DIFFRACTION97.51
1.24-1.260.16071140.13622734X-RAY DIFFRACTION97.33
1.26-1.280.15341270.13662671X-RAY DIFFRACTION96.75
1.28-1.30.16471460.1272687X-RAY DIFFRACTION97.86
1.3-1.330.15411560.12472752X-RAY DIFFRACTION98.04
1.33-1.350.16261320.12242756X-RAY DIFFRACTION98.5
1.35-1.380.15431480.11492706X-RAY DIFFRACTION98.75
1.38-1.410.15291590.11462709X-RAY DIFFRACTION98.29
1.41-1.450.13671550.10762685X-RAY DIFFRACTION97.93
1.45-1.490.14981430.1072693X-RAY DIFFRACTION97.19
1.49-1.530.1061330.10482775X-RAY DIFFRACTION98.81
1.53-1.580.14411230.10572780X-RAY DIFFRACTION99.25
1.58-1.640.1481520.11462725X-RAY DIFFRACTION99.24
1.64-1.70.15191600.11642759X-RAY DIFFRACTION99.02
1.7-1.780.14481320.12662737X-RAY DIFFRACTION97.75
1.78-1.880.1411200.12722714X-RAY DIFFRACTION97.83
1.88-1.990.18581250.13542799X-RAY DIFFRACTION99.12
1.99-2.150.15111630.13552749X-RAY DIFFRACTION99.52
2.15-2.360.18371390.14262757X-RAY DIFFRACTION99.14
2.36-2.70.15331610.15842704X-RAY DIFFRACTION97.32
2.7-3.410.17491320.16492787X-RAY DIFFRACTION98.95
3.41-31.950.15591470.16062775X-RAY DIFFRACTION97.86

+
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