[English] 日本語
Yorodumi
- PDB-9oqx: N-hydroxylamine dehydratase (NohD) H2F/F4P/P5S/R6Y/R144Y/V96A (P1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9oqx
TitleN-hydroxylamine dehydratase (NohD) H2F/F4P/P5S/R6Y/R144Y/V96A (P1/A1/A2) mutant crystal structure with heme
ComponentsN-hydroxylamine dehydratase (NohD)
KeywordsBIOSYNTHETIC PROTEIN / dehydratase / piperazate synthase / heme / N-N bond / hydroxylamine
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesActinomadura luzonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsHiggins, M.A. / Shi, X. / Hoffarth, E.R. / Du, Y.L. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RPGIN-2021-02626 Canada
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Conversion of a Heme-Dependent Dehydratase to a Piperazate Synthase Reveals the Role of the Heme Propionate Group in N-N Bond-Formation.
Authors: Higgins, M.A. / Mirotadze, N. / Shi, X. / Hoffarth, E.R. / Du, Y.L. / Ryan, K.S.
History
DepositionMay 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-hydroxylamine dehydratase (NohD)
B: N-hydroxylamine dehydratase (NohD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6729
Polymers44,9662
Non-polymers1,7057
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-130 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.672, 87.672, 147.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-533-

HOH

-
Components

#1: Protein N-hydroxylamine dehydratase (NohD)


Mass: 22483.180 Da / Num. of mol.: 2 / Mutation: H2F, F4P, P5S, R6Y, R144Y, V96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura luzonensis (bacteria) / Strain: DSM 43766 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.0M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.68→39.21 Å / Num. obs: 66219 / % possible obs: 99.9 % / Redundancy: 27.8 % / Biso Wilson estimate: 34.97 Å2 / CC1/2: 1 / Rpim(I) all: 0.011 / Net I/σ(I): 39.4
Reflection shellResolution: 1.68→1.71 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3291 / CC1/2: 0.72 / Rpim(I) all: 0.607

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→39.21 Å / SU ML: 0.1912 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 1992 3.02 %
Rwork0.1977 63932 -
obs0.1985 65924 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.67 Å2
Refinement stepCycle: LAST / Resolution: 1.68→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 113 345 3481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083271
X-RAY DIFFRACTIONf_angle_d1.06964520
X-RAY DIFFRACTIONf_chiral_restr0.0589488
X-RAY DIFFRACTIONf_plane_restr0.0107589
X-RAY DIFFRACTIONf_dihedral_angle_d11.4114472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.33721400.30354491X-RAY DIFFRACTION99.21
1.72-1.770.2931400.26984478X-RAY DIFFRACTION99.87
1.77-1.820.25051410.25794510X-RAY DIFFRACTION99.98
1.82-1.880.27451400.25454505X-RAY DIFFRACTION99.91
1.88-1.950.35081380.28324466X-RAY DIFFRACTION97.96
1.95-2.020.22131410.2234524X-RAY DIFFRACTION100
2.02-2.120.23021410.21364529X-RAY DIFFRACTION100
2.12-2.230.2261420.22414540X-RAY DIFFRACTION99.74
2.23-2.370.26041390.22864485X-RAY DIFFRACTION98.32
2.37-2.550.2611420.21974571X-RAY DIFFRACTION99.98
2.55-2.810.25351440.21744605X-RAY DIFFRACTION100
2.81-3.210.25781440.21054627X-RAY DIFFRACTION99.98
3.21-4.050.20261460.17814680X-RAY DIFFRACTION99.98
4.05-39.210.18791540.16494921X-RAY DIFFRACTION99.86
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)
15.416902343541.46658921735-2.085781373472.200112346040.2867586290642.655891719990.294459262805-0.5759058204920.1978083688590.168611249-0.396887591821-0.2057105494810.09903400429630.690762262085-0.1120077638840.279124378806-0.0402175413924-0.02351826986110.4750236196090.06759683002560.337915461234-27.4897753253-27.2355382105-13.9001200578
28.28987260498-0.5821926556-0.6024252201075.603486793931.621542853525.015735034390.444299682703-0.1174901601640.4165917829530.0773951954185-0.379816084574-0.02559628729340.3095073402120.3128432020980.001350483127110.139879593351-0.07135904339740.04340450330170.3156590356210.05157926807470.323019131952-17.2931021022-17.0241836153-21.1455913594
33.574628513840.632001660481-0.4802686871052.83026511769-1.610904666033.174994075840.2813326765110.1733932675251.022121729970.236047288216-0.08668967975490.36414057132-0.644772204444-0.159598485149-0.138842306660.2661449321650.03658225598670.07718294387270.3410683996820.09767850488830.533751030843-18.1830867888-8.00238919198-25.8116190467
43.58741039317-2.178222912340.2869393466842.0915266761.664826074245.315629494240.1152321618420.373385803269-0.3242731527960.0779585109241-0.2184778014360.4662186853081.03252076717-0.5160474601940.1260627481050.50889858485-0.0999353338109-0.02902398489880.389916750793-0.009828853833720.275098098795-26.7798287082-40.9461120751-26.3382121813
54.019776130091.65793017789-0.57503289032.56893145792-1.057294241231.810528882330.277394260541-0.05050447000430.6313948728060.160919820488-0.2322422772270.0245537729168-0.2302110228030.200206842419-0.05130900654930.2463399361730.0008105404546830.03483090246950.3419174783810.07946896827610.354987012173-9.8591391993-11.4604904675-23.5729980255
69.051657022551.08384197836-2.533438050228.75612927431-1.423065612467.230072085780.141493834956-0.129540486031-0.3212715116390.101340055895-0.194035562741-0.6421280021640.9598803081370.3410403214510.07228027596860.4311659275430.0114501915607-0.07559361378470.3123300210960.07424186000940.28515835137-19.0506321488-39.1413648158-17.975471056
73.925440849332.038162195030.5591313622033.77204342386-0.9188401625641.79732547899-0.1030086471060.8966925889950.17994762987-0.5062660622850.122939919506-0.07008990811330.0676482626891-0.299714465808-0.108654506490.2756614758270.0417118956594-0.002403836440310.5790595412420.1728342605090.296104524428-21.8547587816-19.4769672078-40.0778819438
81.384781078640.74797534718-0.3135379269371.13397698843-0.4830346333392.745194027720.08850850789720.7063848912360.334965198976-0.04823762213650.06341705369390.1517806745820.144487313747-0.394144773585-0.1250882807520.2534639687370.0215819136364-0.01534325019120.4428207348230.1153281448030.310449302099-24.755503466-20.2458589067-33.0255836283
92.790750217740.2524714427170.4288653584980.9055608587860.2968169053841.610546263520.2448040993280.7950031955480.675990805773-0.082346692556-0.03464640017130.323730348759-0.0601298206366-0.521866839566-0.1988999171880.285619674320.03434312333870.02184405177860.5752310715410.1988052692010.391444031652-25.1399088902-18.2021099127-36.5529493348
105.51958057213-3.17342496394-0.6232953399526.86263321184-0.8107677830115.35258275296-0.1223175276381.12073918339-0.55259769311-0.274414290841-0.2227156128470.346296678840.936772785033-0.3347702966770.3253679548210.532271841369-0.196478637245-0.0290838570250.715350137573-0.06247849636060.301351388593-33.6607312756-39.1206393871-35.7467332525
112.7082964425-0.963064674523-0.6801956627640.476240896293-0.2307014519081.75962939165-0.1061635363260.7997590784170.143421194409-0.2862712947320.2384801175930.5504135508390.556724072597-0.861702890416-0.1194001341570.457158636402-0.172763257693-0.07809586595660.7866960437950.02677957417610.347070595042-35.0227561463-29.0718615705-34.1708173012
127.579335587741.88576959271-2.099665502599.598446774080.4870167496794.48704673842-0.453436119220.215736679471-0.557383262073-0.2650067006920.366725900065-0.3764751355230.2027148658370.8390471140490.1251785347680.2683416057690.06515362213530.07319148762680.5917051031760.07149689348760.311584394938-3.40999701888-24.1010898465-42.6047710285
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 11 )AA1 - 111 - 11
22chain 'A' and (resid 12 through 33 )AA12 - 3312 - 33
33chain 'A' and (resid 34 through 79 )AA34 - 7934 - 79
44chain 'A' and (resid 80 through 97 )AA80 - 9780 - 97
55chain 'A' and (resid 98 through 167 )AA98 - 16798 - 167
66chain 'A' and (resid 168 through 201 )AA168 - 201168 - 201
77chain 'B' and (resid 1 through 33 )BD1 - 331 - 33
88chain 'B' and (resid 34 through 97 )BD34 - 9734 - 97
99chain 'B' and (resid 98 through 113 )BD98 - 11398 - 113
1010chain 'B' and (resid 114 through 138 )BD114 - 138114 - 138
1111chain 'B' and (resid 139 through 167 )BD139 - 167139 - 167
1212chain 'B' and (resid 168 through 201 )BD168 - 201168 - 201

+
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