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- PDB-6m0p: Hydroxylamine oxidoreductase in complex with juglone -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6m0p
TitleHydroxylamine oxidoreductase in complex with juglone
Components
  • Aerobic hydroxylamine oxidoreductase
  • Uncharacterized protein
KeywordsOXIDOREDUCTASE / enhancer / complex
Function / homology
Function and homology information


membrane => GO:0016020 / metal ion binding
Similarity search - Function
: / Hydroxylamine oxidase / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily
Similarity search - Domain/homology
HEME C / Chem-ISW / 5-hydroxynaphthalene-1,4-dione / DI(HYDROXYETHYL)ETHER / Uncharacterized protein / Aerobic hydroxylamine oxidoreductase
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsFujiwara, T. / Fujimoto, Z. / Nishigaya, Y. / Yamazaki, T.
CitationJournal: Appl.Environ.Microbiol. / Year: 2023
Title: Juglone, a plant-derived 1,4-naphthoquinone, binds to hydroxylamine oxidoreductase and inhibits the electron transfer to cytochrome c 554.
Authors: Akutsu, Y. / Fujiwara, T. / Suzuki, R. / Nishigaya, Y. / Yamazaki, T.
History
DepositionFeb 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aerobic hydroxylamine oxidoreductase
B: Uncharacterized protein
C: Aerobic hydroxylamine oxidoreductase
D: Uncharacterized protein
E: Aerobic hydroxylamine oxidoreductase
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,11337
Polymers222,1266
Non-polymers15,98731
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54080 Å2
ΔGint-602 kcal/mol
Surface area55200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.340, 141.070, 106.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLUGLUchain 'A'AA25 - 52625 - 526
221ASPASPGLUGLUchain 'C'CC25 - 52625 - 526
331ASPASPGLUGLUchain 'E'EE25 - 52625 - 526
142SERSERSERSER(chain 'B' and resid 29 through 83)BB29 - 8329 - 83
252SERSERSERSER(chain 'D' and resid 29 through 83)DD29 - 8329 - 83
362SERSERSERSER(chain 'F' and resid 29 through 83)FF29 - 8329 - 83

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Aerobic hydroxylamine oxidoreductase / hydroxylamine oxidoreductase


Mass: 64353.805 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Nitrosomonas europaea (bacteria) / References: UniProt: A0A1I0F3S0
#2: Protein Uncharacterized protein


Mass: 9688.102 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Nitrosomonas europaea (bacteria) / References: UniProt: A0A1H9ZKV8

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Non-polymers , 6 types, 145 molecules

#3: Chemical...
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-ISW / {3,3'-[(9S)-8,13-diethenyl-3,7,12,17-tetramethyl-9,10-dihydroporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~]dipropanoato(2-)}iron / Isoporphyrin containing Fe


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-JUG / 5-hydroxynaphthalene-1,4-dione / Juglone


Mass: 174.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: MES-NaOH, PEG 400, potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 4, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→47.03 Å / Num. obs: 101458 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 46.59 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.394 / Net I/σ(I): 6.74
Reflection shellResolution: 2.78→2.95 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.34 / Num. unique obs: 16383 / CC1/2: 0.622 / Rrim(I) all: 1.98 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1-3660phasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N4N

4n4n


Resolution: 2.78→46.77 Å / SU ML: 0.4759 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 32.6767
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2924 5090 5.02 %Random selection
Rwork0.2556 96311 --
obs0.2575 101401 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.38 Å2
Refinement stepCycle: LAST / Resolution: 2.78→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13300 0 1107 114 14521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003414890
X-RAY DIFFRACTIONf_angle_d1.017720482
X-RAY DIFFRACTIONf_chiral_restr0.03731940
X-RAY DIFFRACTIONf_plane_restr0.00342561
X-RAY DIFFRACTIONf_dihedral_angle_d16.50535366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.810.40131810.39063180X-RAY DIFFRACTION98.94
2.81-2.850.44281570.37883243X-RAY DIFFRACTION99.88
2.85-2.880.40671810.36043191X-RAY DIFFRACTION99.97
2.88-2.920.37881610.3563218X-RAY DIFFRACTION99.85
2.92-2.960.34391630.34263220X-RAY DIFFRACTION99.94
2.96-30.35181680.33233234X-RAY DIFFRACTION99.91
3-3.040.38871890.33523168X-RAY DIFFRACTION99.85
3.04-3.080.37791610.3283202X-RAY DIFFRACTION99.94
3.08-3.130.39081650.32313207X-RAY DIFFRACTION99.94
3.13-3.180.3511760.30733196X-RAY DIFFRACTION99.94
3.18-3.240.30771760.30683216X-RAY DIFFRACTION99.94
3.24-3.30.34041650.30773225X-RAY DIFFRACTION99.91
3.3-3.360.32421590.29893220X-RAY DIFFRACTION99.76
3.36-3.430.31721630.29353224X-RAY DIFFRACTION99.91
3.43-3.50.31541770.28753197X-RAY DIFFRACTION99.97
3.5-3.590.35791810.27863183X-RAY DIFFRACTION99.91
3.59-3.670.33771590.2813237X-RAY DIFFRACTION99.91
3.68-3.770.29241670.26413213X-RAY DIFFRACTION99.94
3.77-3.890.28851820.26073205X-RAY DIFFRACTION99.88
3.89-4.010.32051620.25553206X-RAY DIFFRACTION99.91
4.01-4.150.25471710.23073207X-RAY DIFFRACTION100
4.15-4.320.231600.22293221X-RAY DIFFRACTION100
4.32-4.520.24771710.21363218X-RAY DIFFRACTION100
4.52-4.750.29331760.20833200X-RAY DIFFRACTION100
4.75-5.050.21691660.20023213X-RAY DIFFRACTION100
5.05-5.440.26631760.20873206X-RAY DIFFRACTION100
5.44-5.990.28261740.22233193X-RAY DIFFRACTION100
5.99-6.850.23861620.21233250X-RAY DIFFRACTION100
6.85-8.620.2171720.17683209X-RAY DIFFRACTION100
8.63-46.770.19171690.19133209X-RAY DIFFRACTION99.68
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)
10.489205696826-0.04473606243140.1411060214430.5821064104220.26496511190.595642858098-0.0606492559089-0.840865487320.567883684360.034793941913-0.07493518136080.274320301189-0.1242461122960.0137814944850.1184001092210.4086536443690.177809297077-0.08670561721270.774406924095-0.3868354229440.826479189494-60.347595461349.8918954706-19.9781202859
20.303149270588-0.02723508235960.108122962210.1884806145040.2249739175690.3665003895310.0292334818226-0.7530429385550.4004466188480.187341292076-0.1874755029030.265803553768-0.167127907677-0.1674272648350.1791789741750.5661873778190.0896675805999-0.007585206513141.12326061584-0.6683423876680.952085756972-57.060694258853.1525989505-11.7271024074
30.7409904578790.4070191482210.400932496860.51042223180.1400192872630.2396066286770.0661500046322-0.3777578832020.311049642884-0.0926350591607-0.04692498493970.200169482989-0.142193516249-0.1867334831520.03153363016550.3988315943210.075813308649-0.01596116094310.506177436583-0.2600078960860.487639831936-41.599695233846.5667951731-23.3550018372
40.9867369574440.1188229544880.1650103955890.4093062573730.1445650841970.0674533165197-0.0350333674129-0.3963727810050.863270672601-0.235313497636-0.05164940853930.175072667061-0.198724282749-0.0582235618075-0.03874775495780.4631466744150.0921924477827-0.1003585477520.258696877136-0.3757573656180.641679340032-30.31147992656.5627664999-33.650502406
50.5082425381260.30258466532-0.2235921555121.435398697740.04117454672220.45077843427-0.00149442355079-0.0557595563950.346999624465-0.173813321424-0.08201897453090.566572121125-0.212904797086-0.2081885742080.1090839698710.6208682027580.0580384971786-0.218969758640.250046623691-0.1374229505761.22410176272-19.726145189375.2584268168-37.4172267658
60.05977076361830.0334397389161-0.09103179500890.0904678083999-0.1038313583490.2775032366340.061873757771-0.317250308611-0.3038456391080.0865739327412-0.172475362869-0.1429361034430.3306965155620.0803941767386-0.05368101633430.579438347001-0.09795348882460.02883392484090.8146947004980.7662322451651.16419658596-23.6493961746.08151509523-16.6653708283
70.1561929238870.0110609092308-0.2745265347710.175769334592-0.0003989153897050.456008129241-0.0192243084053-0.709886235009-0.494999797880.0945978131255-0.241049635016-0.2628246172960.1601193304780.321033345764-0.1777233477440.563839106349-0.0662930586264-0.0319277828440.9557622546320.9063071313211.18579926373-30.99868111667.79911943663-10.9166031306
80.564448141266-0.1967487297190.2952828021370.0700672003939-0.1024062317390.24610142453-0.0956426496702-0.449418933783-0.405937021164-0.01409526381730.0351892294493-0.103325419414-0.0467536528781-0.0623754843094-0.1136461490110.4333750304250.1064718257410.08173822192070.4064348883740.364974060420.600129741862-27.812593541223.985460102-22.7482060419
91.416548135060.2188520202930.3050143036180.754065667343-0.02936091053530.397690701278-0.193696671493-0.211501756185-0.531426478164-0.239039490465-0.0382060614891-0.02500551442880.1231603508590.01232970795630.1891150749620.3577216101420.01387872824350.03444883210830.1943920185220.0661217488780.372948633429-36.806586911228.673151288-37.9347060122
104.20397117106-0.414066377652-0.1239071586322.39610190145-0.4650395812473.130164449580.1050348544120.0492026824492-0.719966744625-0.1530563528840.1504854421750.1360676614710.588315040107-0.0428368410317-0.2078607089890.560944750198-0.0184272375895-0.09838201714110.277869250530.02791159580730.487977904535-55.078119443528.7949347614-49.3969987279
110.4726626767060.119277851285-0.4036884292390.431876146211-0.3693319610860.5318390326220.0159336947205-0.7711801912230.2900325336850.161983543923-0.2674388779010.2920035973870.01611834079760.1644121530330.1250903954870.4603492071880.04697460360710.05762069049851.28654571381-0.4480536137510.651108753558-5.5741548527459.548721445-7.16757845207
120.0896288554069-0.0320824895609-0.09418203716460.598044490107-0.3380264930341.71161936798-0.0105154302104-1.167897027260.2130080632840.227384229343-0.2071619152580.030686422137-0.0936203925651-0.0728496469644-0.01137370673990.447504356353-0.0798579764973-0.04792899876221.50076987463-0.2259949163640.494757918176-5.8484837972152.6982757067-0.720417996416
132.3896101170.584043612190.02252433509821.063494583690.1657826703190.344512174183-0.0314701485759-1.121201776340.0860671905651-0.00358167818991-0.1147353100630.0476448022646-0.136539653524-0.04976238829870.06812054191340.2907871402040.0312239392123-0.01771415147080.575053908767-0.1332500237530.4047800765-15.747802045446.9322127874-17.7031223488
141.280275606330.2858733374750.1746103282640.88528353098-0.1605552190090.719010151149-0.0852769310527-0.597288021468-0.378841066222-0.186258235534-0.144038752322-0.239690397480.0116452006708-0.03879209319190.1338013991120.3678498155490.06200186003150.06540309557140.4144120180950.2054114592260.470990892464-9.6458661342436.3390501128-31.2848078164
151.43037746126-0.818600506549-0.1735819041142.9768668398-0.03166563735633.190633656040.0766676844242-0.131352047736-0.1679894550570.241628903294-0.0204781932768-0.7856264482230.02592373044540.506463200787-0.07273817493840.6138168517320.09462374778060.3040162851670.3720422812690.1510334771161.176103126032.9285037285119.8906064177-38.289096018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 120 )
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 236 )
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 309 )
4X-RAY DIFFRACTION4chain 'A' and (resid 310 through 527 )
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 84 )
6X-RAY DIFFRACTION6chain 'C' and (resid 25 through 120 )
7X-RAY DIFFRACTION7chain 'C' and (resid 121 through 236 )
8X-RAY DIFFRACTION8chain 'C' and (resid 237 through 309 )
9X-RAY DIFFRACTION9chain 'C' and (resid 310 through 527 )
10X-RAY DIFFRACTION10chain 'D' and (resid 28 through 83 )
11X-RAY DIFFRACTION11chain 'E' and (resid 25 through 120 )
12X-RAY DIFFRACTION12chain 'E' and (resid 121 through 236 )
13X-RAY DIFFRACTION13chain 'E' and (resid 237 through 309 )
14X-RAY DIFFRACTION14chain 'E' and (resid 310 through 527 )
15X-RAY DIFFRACTION15chain 'F' and (resid 28 through 83 )

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