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- PDB-6ok0: Crystal structure of Sel1 repeat protein from Oxalobacter formigenes -

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Basic information

Entry
Database: PDB / ID: 6ok0
TitleCrystal structure of Sel1 repeat protein from Oxalobacter formigenes
Components(Sel1 repeat protein) x 4
KeywordsHYDROLASE / Sel1 repeat / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologySel1 repeat / Sel1-like repeat / Sel1-like repeats. / beta-lactamase activity / beta-lactamase / Tetratricopeptide-like helical domain superfamily / IMIDAZOLE / TRIETHYLENE GLYCOL / Sel1 repeat protein
Function and homology information
Biological speciesOxalobacter formigenes OXCC13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.174 Å
AuthorsChang, C. / Tesar, C. / Endres, M. / Babnigg, G. / Hassan, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of Sel1 repeat protein from Oxalobacter formigenes
Authors: Chang, C. / Tesar, C. / Endres, M. / Babnigg, G. / Hassan, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sel1 repeat protein
B: Sel1 repeat protein
C: Sel1 repeat protein
D: Sel1 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2727
Polymers64,0184
Non-polymers2553
Water4,306239
1
A: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)16,0211
Polymers16,0211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)15,9811
Polymers15,9811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sel1 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1712
Polymers16,0201
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sel1 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0993
Polymers15,9941
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.768, 68.587, 74.365
Angle α, β, γ (deg.)68.540, 79.250, 89.970
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Sel1 repeat protein


Mass: 16021.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00636 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X8T2, beta-lactamase
#2: Protein Sel1 repeat protein


Mass: 15981.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00636 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X8T2, beta-lactamase
#3: Protein Sel1 repeat protein


Mass: 16020.419 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00636 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X8T2, beta-lactamase
#4: Protein Sel1 repeat protein


Mass: 15994.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00636 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X8T2, beta-lactamase

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Non-polymers , 4 types, 242 molecules

#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium chloride, 0.1M This-HCl, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 37770 / % possible obs: 93.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.061 / Rrim(I) all: 0.151 / Χ2: 0.825 / Net I/σ(I): 7.2 / Num. measured all: 200503
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.17-2.213.10.55315750.7920.3030.6360.85678.6
2.21-2.253.60.50517420.8850.2540.5680.9384.3
2.25-2.293.90.44617220.8930.2170.4990.91787.6
2.29-2.3440.43318570.9140.2070.4820.92991.3
2.34-2.394.30.41819000.9240.1950.4630.89592
2.39-2.444.50.4218830.9320.1940.4650.8793.4
2.44-2.514.60.37518830.9320.1740.4150.8792.9
2.51-2.574.50.36218540.9260.170.4020.89193.7
2.57-2.655.40.33619960.9450.1490.3690.86896.7
2.65-2.735.70.29719460.9580.130.3250.87396.8
2.73-2.835.90.2419490.9710.1040.2620.92896.1
2.83-2.9560.21519450.970.0930.2350.89396.2
2.95-3.085.90.18419370.980.080.2010.86695
3.08-3.246.10.1619450.9740.0690.1750.88795.6
3.24-3.446.40.12919250.9850.0550.140.84496.7
3.44-3.716.30.10719620.9880.0450.1170.82796.7
3.71-4.086.10.09119190.9890.0380.0990.73194.3
4.08-4.676.40.08419620.9880.0360.0920.67396.6
4.67-5.896.30.08119170.9860.0340.0880.60295.6
5.89-506.20.08419510.9840.0360.0920.62695.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.174→39.629 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.39 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2153 1690 4.84 %
Rwork0.1886 56503 -
obs0.1899 35290 73.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.11 Å2 / Biso mean: 36.3395 Å2 / Biso min: 7.81 Å2
Refinement stepCycle: final / Resolution: 2.174→39.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3927 0 16 239 4182
Biso mean--72.41 37.98 -
Num. residues----525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.174-2.20960.2776570.23131254131134
2.2096-2.24770.2369550.21811608166342
2.2477-2.28860.2483890.20991615170445
2.2886-2.33260.24790.22031815189450
2.3326-2.38020.2336980.21462045214354
2.3802-2.4320.28981030.22822087219057
2.432-2.48850.261300.22532228235861
2.4885-2.55080.21061130.22312337245063
2.5508-2.61970.26051280.22652665279373
2.6197-2.69680.23351470.21312834298177
2.6968-2.78380.23821590.21682884304380
2.7838-2.88330.26191440.20623172331684
2.8833-2.99870.23541790.21713007318684
2.9987-3.13510.22061530.20813092324584
3.1351-3.30030.22981820.21313364354692
3.3003-3.5070.19941400.1853477361794
3.507-3.77750.23811630.16743459362294
3.7775-4.15730.20621850.15643296348191
4.1573-4.7580.1512070.14913488369595
4.758-5.99130.20271830.17553367355092
5.9913-39.63580.20981770.18453409358693
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)
10.0247-0.0035-0.02680.02780.01460.03140.00410.1252-0.13660.2012-0.0135-0.09930.0677-0.15800.1690.05270.02910.2259-0.03940.44137.237840.04732.6885
20.4039-0.04810.05420.2054-0.0040.0393-0.01670.2016-0.7429-0.09550.292-0.03630.0459-0.04340.03270.2795-0.0204-0.01270.146-0.02160.356328.368937.79694.9756
30.16920.0944-0.01160.1396-0.11740.1050.15280.0984-0.40310.2683-0.12970.03210.14240.1928-0.00270.16830.0139-0.0130.1375-0.00290.262127.943948.00989.6446
40.0387-0.00280.07050.2306-0.08390.1211-0.10310.0066-0.3720.01350.13930.0990.04060.011-0.00160.10330.0218-0.00890.1590.02610.209227.804157.99367.8179
50.0378-0.0146-0.07490.1366-0.05080.1531-0.01320.2828-0.0381-0.07020.014-0.16210.02740.0999-0.00050.0802-0.0177-0.01740.15290.02470.130334.618565.263.9741
60.60840.0371-0.15290.0369-0.08270.29010.1088-0.29890.0180.1243-0.0893-0.3277-0.09210.0163-0.03980.0482-0.00190.00670.1416-0.01370.255438.619168.73566.7718
70.07220.03210.05650.01150.02190.04570.14380.3513-0.06450.01020.2414-0.0898-0.12670.05890.00110.4287-0.00220.09670.3934-0.02810.254813.151665.0606-22.1011
80.1873-0.11870.0870.38840.06450.0874-0.3367-0.14890.00180.07580.2345-0.29830.10760.1787-0.12640.70760.4004-0.02310.4681-0.32470.332818.526155.3699-16.2284
90.3882-0.15010.19270.6554-0.29360.1934-0.12560.1728-0.04590.2391-0.0478-0.03290.0931-0.4507-0.09190.40140.02130.03710.3262-0.12490.20879.67260.7818-16.6136
100.05880.08850.05710.1950.12950.06790.07240.0336-0.35530.0477-0.0927-0.03710.2738-0.1193-0.02110.40330.00250.01910.2359-0.13620.21585.561657.6169-13.5578
110.4455-0.10390.00580.0531-0.02440.02990.14780.3470.0864-0.0062-0.0321-0.13050.1481-0.0040.00020.2532-0.02580.01020.2268-0.0310.12018.966369.3793-9.3639
120.1499-0.0897-0.08620.05610.03450.1091-0.1060.5782-0.4023-0.2470.16450.60550.2452-0.2635-0.00440.2438-0.0503-0.0230.3684-0.0190.1956-3.932166.7753-9.4544
130.01030.09080.05940.90190.42980.2233-0.23660.01360.0236-0.19950.3362-0.10440.0995-0.04180.42370.19890.0066-0.00620.2610.0110.08584.77975.0767-5.2879
140.0364-0.0851-0.05170.43340.12770.0835-0.20370.40070.1177-0.0602-0.01670.6701-0.0153-0.2725-0.02290.3278-0.0519-0.05290.2870.0490.3425-1.90582.3819-7.8375
150.9587-0.3839-0.62130.25020.44970.87850.0090.00070.4859-0.46570.0365-0.4097-0.61860.44380.02210.390.01280.00620.22660.09150.20474.551588.6337-9.9033
160.03980.03080.01130.016-0.00820.011-0.0143-0.42170.0458-0.0514-0.0619-0.0473-0.1013-0.05070.00010.182-0.048-0.00880.216-0.01730.386415.534101.45812.1495
170.93290.20220.09790.19030.14690.1311-0.08780.22090.6881-0.34670.18810.070.05510.03140.00520.2627-0.0008-0.0250.053-0.02510.65619.0327109.18334.7231
180.1656-0.0609-0.05860.07740.00060.0665-0.1459-0.20290.33880.0860.26210.0229-0.20080.08-0.00060.25690.02040.00630.1602-0.04390.3346.2623101.181312.8101
190.1954-0.19880.04780.1949-0.0970.93240.19270.03680.4485-0.1358-0.05480.0927-0.09420.32180.05420.1226-0.002-0.00760.08910.02010.27816.588693.8575.6112
200.19850.13040.03370.35680.06780.01560.0046-0.0850.39980.439-0.05840.74420.17820.0608-0.00790.20350.00970.03440.19240.04180.21791.328285.593513.3644
210.2044-0.11050.27140.1281-0.13170.38350.0340.0513-0.0413-0.1257-0.0779-0.1075-0.00820.0303-0.00080.06970.00890.00010.1410.02730.187513.869577.35767.5827
220.01860.01570.00820.27390.15680.085-0.0234-0.70670.17010.16240.4172-0.3530.35930.32350.00230.59460.059-0.08030.6135-0.10320.308333.419976.412237.4736
230.0501-0.0542-0.07270.09270.06990.1181-0.1307-0.06530.126-0.05130.2102-0.2639-0.12730.4921-0.01540.3189-0.2910.04240.5887-0.36180.547639.838686.357232.0095
240.5254-0.1012-0.30430.33650.22360.25770.0481-0.16140.1109-0.29590.197-0.264-0.20840.30930.5120.3774-0.06360.04880.3539-0.16690.128731.045180.997731.9156
250.13060.08230.09410.04950.07370.0540.12530.04020.4936-0.01780.0919-0.35-0.41420.0304-0.00040.4505-0.00530.05450.2895-0.08530.266427.965483.420127.8268
260.03820.0067-0.00490.03220.00160.01230.0822-0.24860.13820.13860.019-0.30.06110.0196-00.31240.0097-0.00740.2811-0.00630.174329.28971.63225.6651
270.03-0.03840.01540.0306-0.0110.0065-0.254-0.49280.0458-0.09610.33470.5321-0.3544-0.12510.00010.27780.0477-0.0240.30140.03180.252817.439175.069524.6776
280.4634-0.1427-0.30731.72850.67720.4116-0.3218-0.1059-0.10410.27690.3994-0.268-0.2636-0.00370.39620.226-0.05830.01040.24920.02810.052926.135366.76220.5122
290.2138-0.30780.00421.71080.45370.2021-0.1976-0.0533-0.23130.1469-0.11920.75920.2635-0.3029-0.06340.31340.01130.03140.30010.00820.231718.982859.433223.1927
300.8214-0.06530.06250.04150.1010.41480.02060.0702-0.38820.47070.10280.04830.5056-0.0576-0.01510.4186-0.01730.00680.20130.05280.175926.181453.491625.2263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 20 )A9 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 52 )A21 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 77 )A53 - 77
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 104 )A78 - 104
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 117 )A105 - 117
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 139 )A118 - 139
7X-RAY DIFFRACTION7chain 'B' and (resid 9 through 20 )B9 - 20
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 32 )B21 - 32
9X-RAY DIFFRACTION9chain 'B' and (resid 33 through 45 )B33 - 45
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 64 )B46 - 64
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 77 )B65 - 77
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 88 )B78 - 88
13X-RAY DIFFRACTION13chain 'B' and (resid 89 through 104 )B89 - 104
14X-RAY DIFFRACTION14chain 'B' and (resid 105 through 124 )B105 - 124
15X-RAY DIFFRACTION15chain 'B' and (resid 125 through 139 )B125 - 139
16X-RAY DIFFRACTION16chain 'C' and (resid 9 through 20 )C9 - 20
17X-RAY DIFFRACTION17chain 'C' and (resid 21 through 32 )C21 - 32
18X-RAY DIFFRACTION18chain 'C' and (resid 33 through 52 )C33 - 52
19X-RAY DIFFRACTION19chain 'C' and (resid 53 through 77 )C53 - 77
20X-RAY DIFFRACTION20chain 'C' and (resid 78 through 88 )C78 - 88
21X-RAY DIFFRACTION21chain 'C' and (resid 89 through 139 )C89 - 139
22X-RAY DIFFRACTION22chain 'D' and (resid 8 through 20 )D8 - 20
23X-RAY DIFFRACTION23chain 'D' and (resid 21 through 32 )D21 - 32
24X-RAY DIFFRACTION24chain 'D' and (resid 33 through 45 )D33 - 45
25X-RAY DIFFRACTION25chain 'D' and (resid 46 through 66 )D46 - 66
26X-RAY DIFFRACTION26chain 'D' and (resid 67 through 77 )D67 - 77
27X-RAY DIFFRACTION27chain 'D' and (resid 78 through 88 )D78 - 88
28X-RAY DIFFRACTION28chain 'D' and (resid 89 through 104 )D89 - 104
29X-RAY DIFFRACTION29chain 'D' and (resid 105 through 124 )D105 - 124
30X-RAY DIFFRACTION30chain 'D' and (resid 125 through 139 )D125 - 139

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