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- PDB-4lu9: Crystal structure of E.coli SbcD at 2.5 angstrom resolution -

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Open data


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Basic information

Entry
Database: PDB / ID: 4lu9
TitleCrystal structure of E.coli SbcD at 2.5 angstrom resolution
ComponentsExonuclease subunit SbcD
KeywordsHYDROLASE / meiotic recombination 11 homolog / double-strand break repair protein / nuclease / endonuclease / exonuclease
Function / homologyDouble Stranded RNA Binding Domain - #720 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Double Stranded RNA Binding Domain / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLiu, S. / Tian, L.F. / Yan, X.X. / Liang, D.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis for DNA recognition and nuclease processing by the Mre11 homologue SbcD in double-strand breaks repair.
Authors: Liu, S. / Tian, L.F. / Liu, Y.P. / An, X.M. / Tang, Q. / Yan, X.X. / Liang, D.C.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Exonuclease subunit SbcD
B: Exonuclease subunit SbcD
A: Exonuclease subunit SbcD
D: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,2398
Polymers157,8704
Non-polymers3684
Water10,503583
1
C: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5602
Polymers39,4681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5602
Polymers39,4681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5602
Polymers39,4681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5602
Polymers39,4681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.356, 69.109, 94.233
Angle α, β, γ (deg.)72.35, 84.24, 83.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Exonuclease subunit SbcD / Nuclease SbcCD / D subunit


Mass: 39467.609 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: sbcD, EKO11_3451, KO11_21615 / Production host: Escherichia coli (E. coli) / References: UniProt: E8Y9D8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorDate: Dec 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 49722

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 20.91 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.816 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23463 2467 5 %RANDOM
Rwork0.17553 ---
obs0.17849 47160 98.3 %-
all-49722 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.376 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å2-0.94 Å22.1 Å2
2---2.01 Å20.84 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10332 0 24 583 10939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02110571
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9514427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11151349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.78124.04448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.079151575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4441555
X-RAY DIFFRACTIONr_chiral_restr0.0790.21670
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218080
X-RAY DIFFRACTIONr_mcbond_it0.4081.56791
X-RAY DIFFRACTIONr_mcangle_it0.772210908
X-RAY DIFFRACTIONr_scbond_it1.11533780
X-RAY DIFFRACTIONr_scangle_it1.8564.53519
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 179 -
Rwork0.228 3474 -
obs--97.94 %
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)
12.24992.86512.68375.78475.59466.35090.2129-0.8087-0.80191.13-0.1481-0.79990.95510.0003-0.06480.50210.2031-0.01580.7270.36660.791531.42548.18858.545
21.04060.1778-0.21311.7194-0.15092.40020.0272-0.0140.02260.0343-0.0702-0.28390.0010.29520.0430.04990.00280.00830.06690.00690.055717.11567.67661.736
33.9614-1.329-1.19396.07770.46080.76860.25620.44-0.1111-0.3404-0.2420.06860.17620.1275-0.01410.2910.10870.01560.2948-0.07370.121232.48465.56763.231
46.9852-1.13660.36563.9357-1.191410.33720.0771-0.0392-0.1755-0.35380.07330.63050.0792-0.55-0.15040.1135-0.09030.00250.3018-0.00550.18640.59582.02953.607
53.0516-0.31360.17794.1724-0.77123.21970.04980.04440.0892-0.12640.11730.3762-0.1432-0.2066-0.1670.12830.01030.05010.17-0.02130.086534.32870.11151.81
66.10610.1491-3.97461.7883-2.12879.1640.2876-0.21260.72230.4779-0.14620.2142-0.850.0665-0.14140.1588-0.01320.07610.1132-0.03540.196925.78668.82145.479
70.98030.8915-0.58741.4615-1.12641.00220.1635-0.14060.25060.4936-0.09080.0576-0.50250.0908-0.07270.2826-0.03280.01630.1357-0.04280.164721.22563.99247.031
82.024-0.3134-0.02980.30830.40331.14930.05460.02270.14280.01870.0458-0.1524-0.16280.0689-0.10040.2474-0.04910.01820.2023-0.06940.123517.09660.47546.527
95.3984-13.7832-4.896643.42921.219822.80180.02580.1432-0.4802-0.11070.08051.02570.2174-0.8932-0.10630.5332-0.20310.07170.367-0.07180.3132-3.31175.82229.553
109.8216-3.88784.18942.8503-3.09297.2614-0.2524-0.88360.7270.67010.0137-0.7159-0.58680.62040.23870.5596-0.1735-0.01230.2851-0.09390.419-2.57673.80938.259
111.21512.11450.77313.6924-0.339319.3145-0.2726-0.35580.82960.36930.04580.1256-0.9996-0.28020.22680.6034-0.0788-0.10130.3895-0.31590.8052-7.39282.78736.977
121.82773.56920.60788.56511.43272.16460.1276-0.2453-0.01770.3693-0.0833-0.8252-0.33880.7054-0.04440.5879-0.1330.06780.4355-0.14550.4454-5.37275.07542.067
132.20260.0138-0.56527.55093.58894.4807-0.0394-0.05030.0523-0.2435-0.24370.4379-0.1721-0.27470.28320.01130.0235-0.00960.11960.05190.083233.802674.3927114.6078
140.3635-0.2868-0.17671.82010.10532.22210.0370.0078-0.1089-0.07040.02090.23620.158-0.2885-0.05790.0495-0.01350.00080.08270.01080.075330.31168.2442119.9318
153.48071.7501-0.19483.69370.36560.29510.1837-0.3587-0.28130.2628-0.2257-0.06620.1734-0.1380.0420.249-0.04740.06370.21170.05350.199939.115457.4705114.6328
167.55621.1409-1.93865.9995-0.08579.27670.13720.0602-0.54790.16280.0543-0.55490.34890.4702-0.19150.21730.15060.0870.2090.12160.251158.57759.537120.415
178.56592.14573.25711.28831.66855.68330.08780.2509-1.2699-0.13210.0369-0.2940.97270.3418-0.12470.38980.09060.08450.18370.04430.240343.019350.5667106.5501
184.00781.75-1.41052.6557-2.21132.08110.0363-0.32440.5240.1849-0.0135-0.0214-0.37350.0281-0.02280.2146-0.01930.0220.1487-0.00680.140547.720676.7867113.1402
193.06990.0853-0.05932.65571.54533.70740.086-0.01120.1449-0.0537-0.0219-0.2389-0.17910.283-0.06420.0907-0.01970.02830.12980.03240.118649.4870.6368109.9437
201.7559-1.5344-0.61332.92171.4790.83580.22270.36340.1571-0.8137-0.1716-0.0951-0.4753-0.0833-0.05110.28410.0090.0160.12950.02650.099738.597378.1931107.6413
211.8743-1.0242-0.0365.23011.052.3023-0.02270.11220.0181-0.55860.04030.063-0.29820.0659-0.01760.1340.00420.00960.17730.07330.033233.638376.0996104.1719
222.432-2.4607-3.831411.18511.04648.139-0.18480.5797-0.049-0.69050.06681.28080.425-1.04980.11790.66370.0607-0.03050.26240.15560.379433.8768106.3101109.0359
233.80081.5316-0.26294.0297-0.90742.5744-0.0622-0.17640.87120.06960.00730.3901-0.6552-0.23620.05490.66420.06810.03050.2750.0650.274532.609102.36117.185
241.7935-2.83921.84366.167-2.03845.5267-0.01210.18490.207-0.18850.01210.1838-0.2535-0.22800.66970.03990.02830.27490.14110.312934.280798.3392118.5792
253.2345-6.1896-1.097411.90552.21860.6046-0.0106-0.094-0.3317-0.01950.03560.5791-0.0078-0.2024-0.02510.1554-0.0031-0.00970.26740.06740.213713.32263.469103.828
260.68260.0018-0.18731.24080.25040.7250.0254-0.1524-0.03670.1416-0.00350.0061-0.0089-0.0154-0.02180.0814-0.0046-0.01230.0747-0.01380.100813.8277.72783.662
270.1488-0.40840.25693.2347-1.90381.2625-0.0309-0.1042-0.03020.4248-0.0527-0.1313-0.10730.03730.08350.2002-0.0112-0.00440.15030.00820.16214.3466.14389.565
280.4014-0.37560.65092.1121-3.88488.75020.06530.30960.3023-0.1673-0.0794-0.1764-0.51350.3980.01410.4856-0.0430.08640.37960.08270.4568-16.80278.62880.628
291.6669-3.67682.021413.4742-6.57894.99720.05380.07550.16290.1741-0.4397-0.988-0.14870.58390.38590.094-0.00620.00690.2259-0.02690.3211-8.93768.291.136
301.1859-0.8218-0.25534.3066-0.71782.0552-0.01580.07320.15090.0382-0.1183-0.3939-0.15640.16470.13410.057-0.04830.01590.1126-0.02370.0754-1.92980.10991.351
312.5962-0.0646-1.36243.9292-0.13831.310700.32730.1161-0.3782-0.0158-0.1542-0.03110.08460.01580.168-0.01730.04220.16320.01630.1051-2.62380.4696.269
321.9859-1.64060.25342.7044-0.79240.38450.28730.5188-0.1927-0.4992-0.23680.11720.13350.0359-0.05060.21850.00660.00280.1975-0.06340.09478.62784.26297.009
332.6706-0.08460.61181.12080.17971.72940.14530.43590.1602-0.227-0.19610.02330.00220.00330.05080.1943-0.02250.03550.1507-0.0040.092813.68286.25998.547
340.13840.0345-0.16510.4431-0.12070.2134-0.04610.2710.0019-0.3620.10660.38770.1342-0.3282-0.06050.4646-0.095-0.17340.5380.06080.462514.854116.44493.116
356.939-0.32583.5495.88372.26474.7169-0.030.4032-0.4168-0.73450.11280.61270.6284-0.5891-0.08280.6318-0.3469-0.09960.54160.0320.17118.294105.94489.252
362.4990.64880.91631.6709-0.91953.5262-0.04530.40920.3514-0.2380.15180.6011-0.1821-0.7344-0.10650.24750.0912-0.02380.38010.00410.278616.138112.8482.58
370.66610.2727-0.30881.2844-0.21660.65220.01340.1634-0.0694-0.0882-0.01270.00120.0544-0.038-0.00070.05040.0214-0.02690.09380.00120.083122.4853100.881652.1013
383.002-5.1322-0.754810.42893.06132.29070.0269-0.00870.2128-0.2181-0.0546-0.3726-0.15290.06990.02770.0931-0.0082-0.01430.18840.02820.10936.415795.689346.853
392.2047-0.0665-0.52892.506-0.16492.28790.0306-0.25010.5072-0.01550.03980.2746-0.4835-0.1238-0.07040.10720.0271-0.01610.16260.00870.19247.447117.013758.0245
407.609410.86632.174416.24084.14693.975-0.19230.04940.5327-0.3829-0.07451.046-0.4753-0.65320.26670.13030.0760.03030.26720.04220.283-1.0519109.374454.7365
411.27880.55680.26462.73870.3812.21230.0449-0.19990.31950.0698-0.17990.3626-0.0946-0.26640.1350.07370.03020.04340.114-0.02220.131410.6777108.959862.3351
421.9640.7556-1.26433.93880.34581.33840.0136-0.33090.0470.3036-0.01860.1414-0.0122-0.00890.00510.13930.03350.03870.2476-0.0150.0999.5522106.002666.5015
433.30831.5794-0.02271.55540.27480.2380.2793-0.666-0.1990.4746-0.2481-0.07880.1493-0.0672-0.03120.1849-0.0461-0.01090.21570.04820.095318.118198.779366.3872
440.4092-0.43750.00561.6363-0.25011.7512-0.0818-0.3001-0.00510.1271-0.0123-0.0683-0.0289-0.00470.09410.18370.0290.03130.30660.01610.056222.366294.509466.7351
450.70490.06120.05510.1220.24290.49350.0884-0.3625-0.74210.3291-0.0044-0.07110.66580.0599-0.0840.89920.0579-0.12220.5530.24410.832843.7407106.970185.4059
462.611-0.3942.15130.1286-0.32022.05360.0620.0774-0.25350.04840.0458-0.08450.4020.1818-0.10770.51250.0679-0.0310.45520.08920.371146.147296.543876.085
471.91382.04042.84083.8064.41156.4204-0.1594-0.26860.23420.2410.2915-0.6266-0.3440.7586-0.13210.4941-0.0229-0.24870.7377-0.10820.630746.128108.90476.643
4812.5862-1.84196.4048.122-4.6246.1223-0.2228-0.67430.32580.86260.3669-0.2312-0.05310.2855-0.1440.4480.1929-0.17160.7294-0.17390.285344.1861106.668372.1042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 2
2X-RAY DIFFRACTION2A3 - 109
3X-RAY DIFFRACTION3A110 - 135
4X-RAY DIFFRACTION4A136 - 164
5X-RAY DIFFRACTION5A165 - 218
6X-RAY DIFFRACTION6A219 - 231
7X-RAY DIFFRACTION7A232 - 261
8X-RAY DIFFRACTION8A262 - 283
9X-RAY DIFFRACTION9A284 - 293
10X-RAY DIFFRACTION10A294 - 318
11X-RAY DIFFRACTION11A319 - 327
12X-RAY DIFFRACTION12A328 - 337
13X-RAY DIFFRACTION13B-1 - 18
14X-RAY DIFFRACTION14B19 - 109
15X-RAY DIFFRACTION15B110 - 135
16X-RAY DIFFRACTION16B136 - 164
17X-RAY DIFFRACTION17B165 - 181
18X-RAY DIFFRACTION18B182 - 197
19X-RAY DIFFRACTION19B198 - 231
20X-RAY DIFFRACTION20B232 - 256
21X-RAY DIFFRACTION21B257 - 285
22X-RAY DIFFRACTION22B286 - 295
23X-RAY DIFFRACTION23B296 - 331
24X-RAY DIFFRACTION24B332 - 339
25X-RAY DIFFRACTION25C-2 - 2
26X-RAY DIFFRACTION26C3 - 109
27X-RAY DIFFRACTION27C110 - 134
28X-RAY DIFFRACTION28C135 - 150
29X-RAY DIFFRACTION29C151 - 173
30X-RAY DIFFRACTION30C174 - 203
31X-RAY DIFFRACTION31C204 - 231
32X-RAY DIFFRACTION32C232 - 261
33X-RAY DIFFRACTION33C262 - 284
34X-RAY DIFFRACTION34C285 - 292
35X-RAY DIFFRACTION35C293 - 311
36X-RAY DIFFRACTION36C312 - 339
37X-RAY DIFFRACTION37D-3 - 109
38X-RAY DIFFRACTION38D110 - 122
39X-RAY DIFFRACTION39D123 - 158
40X-RAY DIFFRACTION40D159 - 170
41X-RAY DIFFRACTION41D171 - 205
42X-RAY DIFFRACTION42D206 - 231
43X-RAY DIFFRACTION43D232 - 262
44X-RAY DIFFRACTION44D263 - 282
45X-RAY DIFFRACTION45D283 - 289
46X-RAY DIFFRACTION46D290 - 303
47X-RAY DIFFRACTION47D304 - 329
48X-RAY DIFFRACTION48D330 - 339

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  • 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

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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

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