[English] 日本語
Yorodumi
- PDB-8dos: Crystal structure of Ferredoxin (flavodoxin):NADP(+) oxidoreducta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dos
TitleCrystal structure of Ferredoxin (flavodoxin):NADP(+) oxidoreductase from Klebsiella pneumoniae
ComponentsFlavodoxin/ferredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


flavodoxin-NADP+ reductase / aconitate hydratase activity / succinate dehydrogenase activity / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / heme catabolic process / cellular response to oxidative stress / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
: / Ferredoxin--NADP reductase, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavodoxin/ferredoxin--NADP reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.872 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Ferredoxin (flavodoxin):NADP(+) oxidoreductase from Klebsiella pneumoniae
Authors: Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn / Item: _diffrn.ambient_temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flavodoxin/ferredoxin--NADP reductase
B: Flavodoxin/ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,50911
Polymers57,8702
Non-polymers3,6399
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-43 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.240, 56.020, 56.110
Angle α, β, γ (deg.)106.690, 97.490, 83.400
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Flavodoxin/ferredoxin--NADP reductase / Ferredoxin (flavodoxin):NADP(+) oxidoreductase / Ferredoxin--NADP reductase / Flavodoxin--NADP reductase


Mass: 28935.129 Da / Num. of mol.: 2 / Fragment: KlpnC.00101.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: fpr, BL124_00025130, DRB11_17480, EAO17_13200, G7Z27_00550, GJJ08_000550, GNE24_19530, GNG14_18110, SAMEA3499874_03593, SAMEA3500057_03748, SAMEA3649758_03020, SAMEA3720909_02704, SAMEA3727679_03443, KPHS_29700
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0G3NED2, ferredoxin-NADP+ reductase, flavodoxin-NADP+ reductase

-
Non-polymers , 6 types, 429 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus A9: 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000, 100 mM Tris/BICINE, 30 mM MgCl2 and 30 mM CaCl2, KlpnC.00101.a.B1.PS38694 at 21.7 mg/mL, Tray: plate 12372 well A9 dro 2, Puck: PSL1202, Cryo: DIRECT

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 24, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.872→53.481 Å / Num. obs: 42132 / % possible obs: 93.9 % / Redundancy: 2 % / Biso Wilson estimate: 15.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.07 / Rrim(I) all: 0.102 / Net I/σ(I): 7.9 / Num. measured all: 82827
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.872-1.9040.326390620380.7940.310.4512.291.5
5.081-53.4810.031411521250.9960.0290.04219.994.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX0.97949refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 0.97949 / Resolution: 1.872→27.37 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 20.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 2045 4.86 %
Rwork0.1706 40073 -
obs0.1723 42118 93.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.4 Å2 / Biso mean: 18.8496 Å2 / Biso min: 8.02 Å2
Refinement stepCycle: final / Resolution: 1.872→27.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 237 420 4512
Biso mean--23.78 26.77 -
Num. residues----493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.872-1.920.26921380.2167258892
1.92-1.960.26331350.1979272394
1.96-2.020.24631520.1826263994
2.02-2.080.22331130.1818271893
2.08-2.140.20841170.1778268594
2.14-2.220.23251120.1736266593
2.22-2.310.22791340.1686260192
2.31-2.410.2011260.1676253889
2.41-2.540.21791300.1667275796
2.54-2.70.22051310.1725271596
2.7-2.910.20181560.1699272395
2.91-3.20.19641410.1679266795
3.2-3.660.20731360.1592264392
3.66-4.610.161680.1454272497
4.61-27.370.19191560.1858268795
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)
11.6591-0.079-0.78383.6112-0.07461.2473-0.00010.05270.058-0.12940.0007-0.0671-0.00330.06360.01050.0926-0.0129-0.00470.0889-0.00340.0372-5.393310.4424-34.6137
25.06641.12140.06292.7783-1.19753.97560.0889-0.2380.13230.07670.0059-0.37450.03210.3484-0.03850.07710.0170.01050.144-0.03260.14131.665112.8456-25.6991
32.22010.0267-0.21742.6397-0.10912.0953-0.0307-0.0260.1336-0.1221-0.05020.0012-0.0980.08660.06760.08170.0029-0.00090.07030.0060.0667-4.773813.73-32.5129
45.16033.2979-2.72242.3334-1.70742.2066-0.2233-0.0597-0.3957-0.0303-0.0007-0.16330.33650.09660.21870.15530.01610.01920.0855-0.01220.1074-14.3843-3.7935-22.1323
51.5413-0.0788-0.35292.24080.38041.6608-0.0050.11230.11660.0114-0.00830.13680.0215-0.11760.02170.06060.0042-0.00050.10440.01210.0925-25.37529.1579-27.2084
63.3685-1.22710.922.92740.5871.72320.0349-0.0213-0.09580.22980.11990.4265-0.007-0.2631-0.14930.0677-0.0130.05090.17450.04470.1529-34.46214.5626-17.2839
72.84092.018-0.60572.3415-0.50330.28440.1524-0.21720.08750.1964-0.11280.1192-0.1350.104-0.04370.1644-0.01750.03540.1023-0.01230.1016-22.28998.2646-11.9687
81.3951.7761-0.05575.3612-1.77022.05180.1307-0.2413-0.03860.1266-0.0811-0.20830.02840.1138-0.02450.1467-0.02080.00420.1407-0.01140.0894-16.66440.6731-11.8527
96.48270.9321-4.46313.58840.35515.44950.078-0.04110.4143-0.00180.0190.0709-0.1496-0.0923-0.10610.10770.0192-0.04260.08740.03030.0531-19.336742.5262-1.6615
102.1913-0.5836-0.63142.252-0.39412.3490.1153-0.05240.1586-0.03020.00360.0669-0.0865-0.0317-0.13640.0945-0.004-0.00030.0573-0.0110.0929-14.814637.30331.4888
116.616-2.22261.47144.5353-0.32245.73680.0560.32280.252-0.5030.04960.43880.044-0.3567-0.11170.1596-0.0501-0.02230.13150.0240.1356-24.589132.973-5.7151
122.0356-0.4309-0.36231.7106-0.33451.8704-0.02280.10280.0188-0.11570.01420.04760.0041-0.02020.00620.1072-0.0221-0.00080.07360.00930.0719-17.180738.0366-2.8098
135.2519-5.39324.14756.5064-4.24793.6442-0.1155-0.2841-0.19660.25330.17840.30880.1099-0.2268-0.05850.1612-0.02030.02180.1209-0.02560.0866-13.830721.608411.7555
141.9203-0.3763-0.41692.04550.40011.2724-0.0635-0.12360.03850.20220.0859-0.1240.05440.2177-0.03330.13620.00180.00370.0777-0.00930.0942-4.059825.63158.257
150.9657-0.814-0.34141.0258-1.40398.5698-0.03810.04350.14770.00040.0786-0.2704-0.29710.3543-0.04110.1159-0.05160.02550.1012-0.00510.16611.486633.91811.6404
161.74730.3464-0.30992.0259-0.49712.6288-0.1170.1535-0.1502-0.19460.0619-0.39620.13610.16970.05780.085-0.00050.01540.1303-0.01020.17185.639319.7867-0.1095
171.45-0.90372.11250.9353-1.5434.7270.0593-0.0151-0.1157-0.0565-0.00670.04710.12930.0581-0.05450.1636-0.00790.03020.0922-0.00310.0959-5.692813.0829-1.282
180.87210.17131.01882.7183-2.64914.51360.1540.0097-0.1270.0307-0.04250.21330.0934-0.2482-0.09020.1688-0.01080.02590.1095-0.010.1049-12.081913.11474.4351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 35 )A2 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 53 )A36 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 91 )A54 - 91
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 107 )A92 - 107
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 190 )A108 - 190
6X-RAY DIFFRACTION6chain 'A' and (resid 191 through 206 )A191 - 206
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 229 )A207 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 248 )A230 - 248
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 14 )B3 - 14
10X-RAY DIFFRACTION10chain 'B' and (resid 15 through 35 )B15 - 35
11X-RAY DIFFRACTION11chain 'B' and (resid 36 through 53 )B36 - 53
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 91 )B54 - 91
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 107 )B92 - 107
14X-RAY DIFFRACTION14chain 'B' and (resid 108 through 143 )B108 - 143
15X-RAY DIFFRACTION15chain 'B' and (resid 144 through 162 )B144 - 162
16X-RAY DIFFRACTION16chain 'B' and (resid 163 through 206 )B163 - 206
17X-RAY DIFFRACTION17chain 'B' and (resid 207 through 229 )B207 - 229
18X-RAY DIFFRACTION18chain 'B' and (resid 230 through 248 )B230 - 248

+
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