[English] 日本語
Yorodumi
- PDB-6n1f: Crystal structure of Oxidoreductase, 2OG-Fe(II) oxygenase family,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n1f
TitleCrystal structure of Oxidoreductase, 2OG-Fe(II) oxygenase family, from Burkholderia pseudomallei
ComponentsOxidoreductase, 2OG-Fe(II) oxygenase family
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology2OG-Fe(II) oxygenase superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / oxidoreductase activity / : / Oxidoreductase, 2OG-Fe(II) oxygenase family
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Oxidoreductase, 2OG-Fe(II) oxygenase family, from Burkholderia pseudomallei
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D. / Edwards, T.E.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oxidoreductase, 2OG-Fe(II) oxygenase family
B: Oxidoreductase, 2OG-Fe(II) oxygenase family
C: Oxidoreductase, 2OG-Fe(II) oxygenase family
D: Oxidoreductase, 2OG-Fe(II) oxygenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,52310
Polymers108,2284
Non-polymers2946
Water7,963442
1
A: Oxidoreductase, 2OG-Fe(II) oxygenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1483
Polymers27,0571
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidoreductase, 2OG-Fe(II) oxygenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1132
Polymers27,0571
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxidoreductase, 2OG-Fe(II) oxygenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1483
Polymers27,0571
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Oxidoreductase, 2OG-Fe(II) oxygenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1132
Polymers27,0571
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Oxidoreductase, 2OG-Fe(II) oxygenase family
B: Oxidoreductase, 2OG-Fe(II) oxygenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2615
Polymers54,1142
Non-polymers1473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-39 kcal/mol
Surface area17910 Å2
MethodPISA
6
C: Oxidoreductase, 2OG-Fe(II) oxygenase family
hetero molecules

D: Oxidoreductase, 2OG-Fe(II) oxygenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2615
Polymers54,1142
Non-polymers1473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1590 Å2
ΔGint-41 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.030, 54.990, 112.100
Angle α, β, γ (deg.)77.660, 87.030, 64.730
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Oxidoreductase, 2OG-Fe(II) oxygenase family /


Mass: 27057.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_A2398 / Plasmid: BupsA.17629.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3JFV4
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Hampton Research PACT screen F12: 200mM sodium malonate dibasic, 20% PEG 3350, 100mM BisTris propane/HCl pH 6.5: BupsA.17629.a.A1.PD38303 at 10.9mg/ml: cryo: 20% EG: tray 299888F12: puck WTM5-3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 1, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.05→27.351 Å / Num. obs: 59902 / % possible obs: 96.3 % / Redundancy: 3.814 % / Biso Wilson estimate: 34.439 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.081 / Χ2: 1 / Net I/σ(I): 11.64 / Num. measured all: 228439 / Scaling rejects: 59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.13.3390.3453.1740150.9120.41387.5
2.1-2.163.5330.3043.7643450.9270.3696.9
2.16-2.223.930.2524.9642500.9550.29297.2
2.22-2.293.9570.2095.9241120.9670.24296.8
2.29-2.373.9510.1826.5440250.9780.2198.1
2.37-2.453.9390.1557.5938210.9820.1897.6
2.45-2.543.9280.1388.3637810.9850.1697.1
2.54-2.653.9180.1189.635930.9870.13797.5
2.65-2.763.9060.09611.2734790.9910.11297.7
2.76-2.93.8940.08812.1632890.9930.10297.5
2.9-3.063.8820.07114.631340.9950.08397.5
3.06-3.243.8340.06217.129790.9950.07297.6
3.24-3.473.8630.05419.3727620.9950.06397.3
3.47-3.743.8530.04920.6225980.9970.05797.9
3.74-4.13.8080.04921.8223600.9960.05796.6
4.1-4.583.8010.04723.1521670.9960.05496.7
4.58-5.293.7360.04722.9718620.9960.05596.6
5.29-6.483.6820.05221.8815430.9950.0694.4
6.48-9.173.5770.05122.2311930.9950.0692.2
9.17-27.3513.4190.05122.665940.9960.0686.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3304)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.05→27.351 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.51
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 2024 3.38 %0
Rwork0.2078 ---
obs0.209 59870 96.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.83 Å2 / Biso mean: 36.0431 Å2 / Biso min: 5.63 Å2
Refinement stepCycle: final / Resolution: 2.05→27.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6467 0 6 445 6918
Biso mean--39.82 37.47 -
Num. residues----832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066626
X-RAY DIFFRACTIONf_angle_d0.8598993
X-RAY DIFFRACTIONf_dihedral_angle_d13.2743935
X-RAY DIFFRACTIONf_chiral_restr0.052978
X-RAY DIFFRACTIONf_plane_restr0.0041206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10130.29811260.26323718384487
2.1013-2.15810.281460.25764179432597
2.1581-2.22150.29491340.24734174430897
2.2215-2.29320.31011490.23824166431597
2.2932-2.37510.30511610.24464185434698
2.3751-2.47020.29131300.23734208433898
2.4702-2.58250.28191490.2424153430298
2.5825-2.71850.28881640.23954182434698
2.7185-2.88870.28861540.24244189434398
2.8887-3.11140.2721270.22114202432997
3.1114-3.4240.24891290.20554202433197
3.424-3.91830.21711920.18584142433497
3.9183-4.93190.16921240.15414143426797
4.9319-27.3530.1761390.19044003414293
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.93992.14220.57488.36831.91924.2165-0.1726-0.25620.25330.11120.07950.4452-0.10930.22930.11670.21110.00550.01070.2351-0.02890.229-1.625910.35341.9165
22.49691.0271-0.25043.22670.92423.2399-0.04510.1607-0.02910.3896-0.08470.29170.1241-0.09210.10350.2249-0.0067-0.00820.1041-0.01850.2541-14.29223.417143.9761
32.4361.0018-0.00545.7106-2.03272.4991-0.0717-0.15040.24871.38520.00531.0528-0.066-0.30380.02450.4756-0.02330.23380.3048-0.09070.6345-27.052714.322655.8109
41.1816-0.6389-0.07383.92070.41421.6884-0.017-0.15990.08830.8068-0.11560.22420.279-0.11150.13470.4539-0.07230.04220.2332-0.01790.2597-17.52115.498155.5291
56.74351.91770.42445.08692.39672.9023-0.27940.62160.5922-0.3646-0.03850.0021-0.1671-0.22680.1670.2622-0.0157-0.06520.2541-0.03670.2399-15.571413.071544.3902
62.1150.8156-1.91024.02850.94792.47690.1983-0.4728-0.23580.4206-0.096-0.5399-0.03830.25320.02680.2162-0.0314-0.13610.21040.0230.2423-5.707915.331146.9608
73.38240.4212-0.41553.92590.56562.08710.002-0.67170.22031.2221-0.17490.04460.03740.39120.08270.3615-0.0745-0.09430.29890.00530.2191-7.724513.05253.3925
83.3513-1.28251.28014.9849-0.63213.2469-0.0519-0.26370.00960.75390.02230.06730.1829-0.49110.06130.3021-0.04370.03150.2017-0.04920.2706-16.39211.274455.7205
91.76710.61820.06846.3716-1.24173.42960.08960.0388-0.4198-0.08940.1683-0.0251-0.0172-0.1415-0.12420.1872-0.0156-0.00640.1453-0.00460.2788-16.8916-21.910641.8178
101.707-1.10490.54882.6609-2.052.4596-0.080.0339-0.00010.00140.02220.0176-0.0358-0.10510.03130.1738-0.0145-0.03370.1732-0.03480.1985-12.921-11.479733.522
112.1532-0.5126-0.04982.79290.04382.93640.09680.4967-0.0786-0.3709-0.1312-0.2080.30450.1956-0.01370.20140.00760.00690.3209-0.0340.2407-5.4755-13.053221.3362
123.47351.4912-0.66793.3697-0.79152.0022-0.0898-0.0191-0.362-0.3005-0.0459-0.37210.36230.08180.13110.26270.06240.02840.3363-0.0950.2509-6.7897-22.073424.7419
133.81190.6868-0.29664.3926-0.65313.46290.02650.34-0.3586-0.2624-0.10480.14160.4523-0.17810.03120.187-0.0234-0.00430.2172-0.07230.2249-15.1358-23.710631.2582
142.203-0.0861-0.03032.1241-0.58313.5126-0.08720.08060.2455-0.267-0.1054-0.20160.36340.18840.14260.23370.03570.02510.2537-0.00970.2103-6.7353-19.508524.4347
152.0652-0.80280.41523.10620.5031.6879-0.02870.20.0944-0.19890.0169-0.3365-0.02240.05890.00910.20780.00850.06830.18060.01060.290718.8826-4.476687.2359
166.304-1.031.86310.1936-0.40270.91290.2084-0.1677-0.1066-0.5729-0.22490.5094-0.3839-0.66820.04980.22120.0167-0.04080.3151-0.09290.4243-4.0157-1.356487.3809
172.6794-1.38271.33568.1633-1.46423.11030.2113-0.1021-0.3634-0.9406-0.47211.14760.4066-0.390.1670.4434-0.0321-0.0790.4077-0.09690.5415-4.8339-15.631477.4441
181.5510.47380.22943.81510.28161.32570.03270.177-0.0761-0.8119-0.1374-0.0162-0.1995-0.1380.15010.4440.06090.00720.225-0.00970.23225.4625-3.771574.5521
192.2148-0.54951.61167.4119-0.17391.3435-0.0643-0.2627-0.28280.4022-0.07040.14380.1696-0.29950.07650.2615-0.03150.08970.2372-0.04080.23917.9231-10.967785.9288
202.3543-0.74922.30065.36870.90242.8536-0.11130.4440.1808-0.36920.1891-0.38240.28480.4530.02320.2125-0.01560.09770.21440.01650.210818.0628-13.70983.3557
215.88210.10431.19316.97860.87293.6950.13090.0904-0.2709-0.4189-0.1779-0.17040.161-0.02570.04890.20630.01310.03160.1385-0.01880.199911.198-15.193682.0941
224.93581.9045-0.93994.88770.19264.3661-0.09640.7401-0.0551-1.288-0.12360.0844-0.5932-0.14260.12970.51960.076-0.01770.2543-0.04360.28928.3031-3.094968.545
233.4222-3.8779-2.20925.51022.99224.07380.17010.0270.61-0.01140.0976-0.5644-0.10390.007-0.26320.27980.05190.03870.18760.04080.3895-17.0033-25.655888.9104
241.39261.211-0.52462.0651-0.97732.6953-0.096-0.02370.0668-0.08750.0697-0.07870.1665-0.0590.07180.16510.03560.05150.1805-0.02120.263-13.0441-36.72697.5713
251.68910.1861-0.79072.0894-0.13663.4277-0.1017-0.52260.07770.3358-0.0373-0.2487-0.17890.49510.15930.19730.009-0.05010.3134-0.03660.2852-6.4076-33.7404109.7281
261.49870.2997-0.04822.0554-0.61871.80360.22380.24090.28830.2548-0.102-0.5515-0.24360.4306-0.01060.1257-0.044-0.00870.4071-0.02250.3323-2.6698-32.2969104.1102
275.04441.1192-1.524.3182-0.57814.2038-0.1835-0.07220.1331-0.0560.2264-0.0673-0.31630.2279-0.01170.2857-0.0237-0.0190.3496-0.11870.3125-17.4004-20.1712109.3374
281.37740.59091.64462.39080.44822.0012-0.1668-0.65741.09290.2266-0.03380.0033-0.49750.533-0.01810.2114-0.0831-0.02690.391-0.07510.4851-3.7538-26.1894102.9782
291.5527-1.86421.19793.4441-0.0362.59370.0104-0.31150.1860.1041-0.02410.2355-0.1651-0.08320.01560.13750.00730.02180.2324-0.03630.3009-18.648-24.373698.866
304.2555-0.0721-1.65353.6029-0.10953.6060.0256-0.33830.150.3516-0.0850.2797-0.3764-0.43120.0450.19820.04980.01150.2626-0.02230.1986-16.4484-24.0131103.0844
314.91770.53991.39941.87310.31431.44750.2147-0.30020.49560.2073-0.2859-0.4977-0.51650.70750.06740.2382-0.1579-0.04030.43910.0050.51280.976-28.7742105.6471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 16 )A3 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 50 )A17 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 76 )A51 - 76
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 144 )A77 - 144
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 159 )A145 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 178 )A160 - 178
7X-RAY DIFFRACTION7chain 'A' and (resid 179 through 190 )A179 - 190
8X-RAY DIFFRACTION8chain 'A' and (resid 191 through 216 )A191 - 216
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 16 )B3 - 16
10X-RAY DIFFRACTION10chain 'B' and (resid 17 through 50 )B17 - 50
11X-RAY DIFFRACTION11chain 'B' and (resid 51 through 109 )B51 - 109
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 144 )B110 - 144
13X-RAY DIFFRACTION13chain 'B' and (resid 145 through 192 )B145 - 192
14X-RAY DIFFRACTION14chain 'B' and (resid 193 through 214 )B193 - 214
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 37 )C3 - 37
16X-RAY DIFFRACTION16chain 'C' and (resid 38 through 50 )C38 - 50
17X-RAY DIFFRACTION17chain 'C' and (resid 51 through 71 )C51 - 71
18X-RAY DIFFRACTION18chain 'C' and (resid 72 through 144 )C72 - 144
19X-RAY DIFFRACTION19chain 'C' and (resid 145 through 159 )C145 - 159
20X-RAY DIFFRACTION20chain 'C' and (resid 160 through 178 )C160 - 178
21X-RAY DIFFRACTION21chain 'C' and (resid 179 through 199 )C179 - 199
22X-RAY DIFFRACTION22chain 'C' and (resid 200 through 215 )C200 - 215
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 16 )D3 - 16
24X-RAY DIFFRACTION24chain 'D' and (resid 17 through 50 )D17 - 50
25X-RAY DIFFRACTION25chain 'D' and (resid 51 through 109 )D51 - 109
26X-RAY DIFFRACTION26chain 'D' and (resid 110 through 124 )D110 - 124
27X-RAY DIFFRACTION27chain 'D' and (resid 125 through 135 )D125 - 135
28X-RAY DIFFRACTION28chain 'D' and (resid 136 through 150 )D136 - 150
29X-RAY DIFFRACTION29chain 'D' and (resid 151 through 178 )D151 - 178
30X-RAY DIFFRACTION30chain 'D' and (resid 179 through 199 )D179 - 199
31X-RAY DIFFRACTION31chain 'D' and (resid 200 through 215 )D200 - 215

+
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