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- PDB-9ovf: Rubredoxin covalently linked to benzo-18-crown-6 -

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Basic information

Entry
Database: PDB / ID: 9ovf
TitleRubredoxin covalently linked to benzo-18-crown-6
ComponentsRubredoxin-1
KeywordsMETAL BINDING PROTEIN / benzo-18-crown-6 / Cys arylation / site-selective protein modification
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding / cytoplasm
Similarity search - Function
: / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile.
Similarity search - Domain/homology
: / ACETATE ION / : / Rubredoxin-1
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans ATCC 27774 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsAdhami, N. / Sawaya, M.R. / Shafaat, H.S. / Rodriguez, J.A. / Spokoyny, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM124746-08 United States
CitationJournal: To Be Published
Title: Site-selective Au(III)-mediated metalloenzyme conjugations
Authors: Adhami, N. / Rebelo, M.J.P. / Teptarkulkarn, H. / Ando, S.H. / Olivares, E.J. / Goff, T.L. / Munoz, A.J. / Qu, S. / Kerr, T.A. / Coutinho, R.J. / Sawaya, M.R. / Shafaat, H.S. / Rodrigues, J.A. / Spokoyny, M.A.
History
DepositionMay 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rubredoxin-1
B: Rubredoxin-1
C: Rubredoxin-1
D: Rubredoxin-1
E: Rubredoxin-1
F: Rubredoxin-1
G: Rubredoxin-1
H: Rubredoxin-1
I: Rubredoxin-1
J: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,19889
Polymers51,17710
Non-polymers9,02279
Water3,081171
1
A: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,75110
Polymers5,1181
Non-polymers6339
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1768
Polymers5,1181
Non-polymers2,0587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7289
Polymers5,1181
Non-polymers6108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7289
Polymers5,1181
Non-polymers6108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,25810
Polymers5,1181
Non-polymers2,1409
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,75110
Polymers5,1181
Non-polymers6339
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7289
Polymers5,1181
Non-polymers6108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6467
Polymers5,1181
Non-polymers5286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,75110
Polymers5,1181
Non-polymers6339
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Rubredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6827
Polymers5,1181
Non-polymers5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.000, 89.150, 94.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 13 or (resid 14...
d_2ens_1(chain "B" and (resid 2 through 13 or (resid 14...
d_3ens_1(chain "C" and (resid 2 through 13 or (resid 14...
d_4ens_1(chain "D" and (resid 2 through 13 or (resid 14...
d_5ens_1(chain "E" and (resid 2 through 13 or (resid 14...
d_6ens_1(chain "F" and (resid 2 through 13 or (resid 14...
d_7ens_1(chain "G" and (resid 2 through 20 or (resid 21...
d_8ens_1(chain "H" and (resid 2 through 13 or (resid 14...
d_9ens_1(chain "I" and (resid 2 through 13 or (resid 14...
d_10ens_1(chain "J" and (resid 2 through 13 or (resid 14...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNASPASPAA2 - 282 - 28
d_12TRPTRPALAALAAA30 - 4530 - 45
d_13FEFEFEFEAK101
d_14LIGLIGLIGLIGAL102
d_15NANANANAAM103
d_16ACTACTACTACTAN104
d_21GLNGLNASPASPBB2 - 282 - 28
d_22TRPTRPALAALABB30 - 4530 - 45
d_23FEFEFEFEBP101
d_24LIGLIGLIGLIGBQ102
d_25NANANANABR103
d_26ACTACTACTACTBS104
d_31GLNGLNASPASPCC2 - 282 - 28
d_32TRPTRPALAALACC30 - 4530 - 45
d_33FEFEFEFECV101
d_34LIGLIGLIGLIGCW102
d_35NANANANACX103
d_36ACTACTACTACTCY104
d_41GLNGLNASPASPDD2 - 282 - 28
d_42TRPTRPALAALADD30 - 4530 - 45
d_43FEFEFEFEDBA101
d_44LIGLIGLIGLIGDCA102
d_45NANANANADDA103
d_46ACTACTACTACTDEA104
d_51GLNGLNASPASPEE2 - 282 - 28
d_52TRPTRPALAALAEE30 - 4530 - 45
d_53FEFEFEFEEGA101
d_54LIGLIGLIGLIGEHA102
d_55NANANANAEIA103
d_56ACTACTACTACTEJA104
d_61GLNGLNASPASPFF2 - 282 - 28
d_62TRPTRPALAALAFF30 - 4530 - 45
d_63FEFEFEFEFLA101
d_64LIGLIGLIGLIGFMA102
d_65NANANANAFNA103
d_66ACTACTACTACTFOA104
d_71GLNGLNASPASPGG2 - 282 - 28
d_72TRPTRPALAALAGG30 - 4530 - 45
d_73FEFEFEFEGQA101
d_74LIGLIGLIGLIGGRA102
d_75NANANANAGSA103
d_76ACTACTACTACTGTA104
d_81GLNGLNASPASPHH2 - 282 - 28
d_82TRPTRPALAALAHH30 - 4530 - 45
d_83FEFEFEFEHUA101
d_84LIGLIGLIGLIGHVA102
d_85NANANANAHWA103
d_86ACTACTACTACTHXA104
d_91GLNGLNASPASPII2 - 282 - 28
d_92TRPTRPALAALAII30 - 4530 - 45
d_93FEFEFEFEIYA101
d_94LIGLIGLIGLIGIZA102
d_95NANANANAIAB103
d_96ACTACTACTACTIBB104
d_101GLNGLNASPASPJJ2 - 281 - 27
d_102TRPTRPALAALAJJ30 - 4529 - 44
d_103FEFEFEFEJDB101
d_104LIGLIGLIGLIGJEB102
d_105NANANANAJFB103
d_106ACTACTACTACTJGB104

NCS oper:
IDCodeMatrixVector
1given(0.349917764523, -0.936779839299, 0.00104439131346), (0.936774225502, 0.349919287522, 0.00324694551704), (-0.00340712576397, -0.000157805053062, 0.999994183279)52.5593913841, 15.0436448757, 0.0947775160108
2given(-0.791767862505, -0.609979228456, -0.0320779169512), (0.609837258749, -0.792381435772, 0.0151716210301), (-0.0346723195807, -0.00754990698615, 0.999370216266)56.7537117462, 70.7780009952, 0.771905797641
3given(-0.804459784136, 0.590042107013, -0.0685183746176), (-0.586850043155, -0.80731405664, -0.0620567546767), (-0.0919319452508, -0.00971215237016, 0.995717927698)4.92792506654, 93.5299786217, 1.63413834669
4given(0.300066652554, 0.953769020546, 0.0168718544126), (-0.949620284538, 0.300345026106, -0.0895219553339), (-0.0904506452102, 0.0108406982791, 0.99584193527)-33.1325265349, 50.6582282295, 0.764183535423
5given(0.673285405009, -0.737121274111, 0.0577839999875), (-0.737102549806, -0.675289071114, -0.0257779266632), (0.0580223618227, -0.025236831935, -0.997996246407)35.9880826777, 88.1288216977, 83.0915018821
6given(-0.508942421479, -0.86041736714, -0.0256820159232), (-0.858518568333, 0.509538244349, -0.0575903235993), (0.0626376839089, -0.00726167120409, -0.998009914122)63.6742264216, 38.2244405955, 82.4139729933
7given(-0.965241351794, 0.260722320985, -0.0182484006835), (0.260138757801, 0.965128121191, 0.0292495534227), (0.0252380561226, 0.0234857621995, -0.999405553065)20.1751683756, -3.86418875915, 81.8053040677
8given(-0.101616327008, 0.994769017973, 0.0104270305498), (0.993857033404, 0.101050078765, 0.0451340086336), (0.0438442611873, 0.0149493298299, -0.998926522973)-28.3076467187, 23.1891795342, 81.7679522318
9given(0.922756159511, 0.38228322401, 0.0487914615948), (0.381187137746, -0.923996405015, 0.0304468313021), (0.0567224479401, -0.0094963235298, -0.998344822063)-18.2769428916, 79.4181558589, 82.5847091175

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Components

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Protein/peptide , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein/peptide
Rubredoxin-1 / Rd-1


Mass: 5117.656 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans ATCC 27774 (bacteria)
Gene: rd1, Ddes_2011 / Production host: Escherichia coli (E. coli) / References: UniProt: P04170

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Non-polymers , 6 types, 250 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-A1CET / 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol


Mass: 344.423 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H24O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.3 % / Description: chunky
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Sodium acetate trihydrate , 0.1 M Sodium citrate 5.5 , 5 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92025 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92025 Å / Relative weight: 1
ReflectionResolution: 1.45→64.93 Å / Num. obs: 93529 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.141 / Net I/σ(I): 12.64
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.45-1.492.25467970.3772.3531
1.49-1.531.78966930.591.8581
1.53-1.571.47864710.6691.5361
1.57-1.621.25363180.7411.3041
1.62-1.670.88960970.8940.9251
1.67-1.730.69359280.9250.7191
1.73-1.80.5957210.940.6121
1.8-1.870.46955310.9610.4871
1.87-1.960.37652760.9740.391
1.96-2.050.29850780.9840.311
2.05-2.160.22148380.990.231
2.16-2.290.1745790.9940.1771
2.29-2.450.14643040.9960.1521
2.45-2.650.12640400.9970.1311
2.65-2.90.09637170.9980.11
2.9-3.240.07133760.9980.0741
3.24-3.740.05330080.9990.0551
3.74-4.590.04225520.9990.0431
4.59-6.490.04220280.9990.0431
6.49-64.930.03711770.9990.0391

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XSCALE20241002data scaling
XDS20241002data reduction
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→51.88 Å / SU ML: 0.1579 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2119 9350 10 %
Rwork0.199 84156 -
obs0.2003 93506 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.65 Å2
Refinement stepCycle: LAST / Resolution: 1.45→51.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 512 171 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00564100
X-RAY DIFFRACTIONf_angle_d0.8395482
X-RAY DIFFRACTIONf_chiral_restr0.0931484
X-RAY DIFFRACTIONf_plane_restr0.0059727
X-RAY DIFFRACTIONf_dihedral_angle_d12.87511686
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.56326754482
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.64310430602
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.800679708835
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.786767425892
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.925170424193
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.642912347546
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.627672130998
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS0.582934929995
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS0.808825565146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.32453030.3172725X-RAY DIFFRACTION97.93
1.47-1.480.32053100.30662792X-RAY DIFFRACTION99.94
1.48-1.50.29863060.28962750X-RAY DIFFRACTION99.87
1.5-1.520.28813060.272752X-RAY DIFFRACTION99.87
1.52-1.540.27243070.24852767X-RAY DIFFRACTION99.9
1.54-1.560.24923100.2432789X-RAY DIFFRACTION100
1.56-1.580.23573090.22812777X-RAY DIFFRACTION100
1.58-1.610.2393080.22782777X-RAY DIFFRACTION100
1.61-1.630.25063100.23762794X-RAY DIFFRACTION99.87
1.63-1.660.2313070.20662772X-RAY DIFFRACTION99.9
1.66-1.690.22273090.20092782X-RAY DIFFRACTION99.97
1.69-1.720.23193130.19762812X-RAY DIFFRACTION100
1.72-1.750.20643080.19962772X-RAY DIFFRACTION100
1.75-1.790.20433070.18132769X-RAY DIFFRACTION100
1.79-1.830.19653110.1822801X-RAY DIFFRACTION99.97
1.83-1.870.19113110.17822796X-RAY DIFFRACTION100
1.87-1.920.19793090.1722779X-RAY DIFFRACTION100
1.92-1.970.18413110.17072797X-RAY DIFFRACTION100
1.97-2.030.1813140.17422825X-RAY DIFFRACTION100
2.03-2.090.19973100.17252790X-RAY DIFFRACTION100
2.09-2.170.19893110.18852801X-RAY DIFFRACTION100
2.17-2.250.18313130.16842816X-RAY DIFFRACTION100
2.25-2.360.1923110.1782806X-RAY DIFFRACTION100
2.36-2.480.20063150.18342834X-RAY DIFFRACTION100
2.48-2.630.20153130.19052817X-RAY DIFFRACTION99.87
2.63-2.840.20943140.20132831X-RAY DIFFRACTION99.97
2.84-3.120.21833160.20452847X-RAY DIFFRACTION100
3.12-3.580.19093180.19542854X-RAY DIFFRACTION99.97
3.58-4.50.19263240.17982923X-RAY DIFFRACTION100
4.5-51.880.24163360.22723009X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: 15.3698032584 Å / Origin y: 45.2270840619 Å / Origin z: 41.6934259159 Å
111213212223313233
T0.111321527578 Å2-0.00322223880975 Å20.0029851654036 Å2-0.11194956155 Å2-0.0059505464609 Å2--0.11719214854 Å2
L0.445118693848 °2-0.0277282085461 °2-0.120235095715 °2-0.439779459003 °20.0765019097631 °2--0.622201733601 °2
S-0.024396853525 Å °0.038382515155 Å °-0.0173040678216 Å °0.013821602985 Å °-0.00308212521585 Å °-0.0208313165371 Å °0.0450411358369 Å °-0.0046985838493 Å °-0.000216493908024 Å °
Refinement TLS groupSelection details: all

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