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- PDB-3sl7: Crystal structure of CBS-pair protein, CBSX2 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 3sl7
TitleCrystal structure of CBS-pair protein, CBSX2 from Arabidopsis thaliana
ComponentsCBS domain-containing protein CBSX2
KeywordsMEMBRANE PROTEIN / CBS-pair protein / redox regulator / plant CBS domain / Thioredoxin / Chloroplast
Function / homology
Function and homology information


chloroplast stroma / chloroplast / cell redox homeostasis / plasma membrane
Similarity search - Function
CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CBS domain-containing protein CBSX2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.905 Å
AuthorsJeong, B.-C. / Lee, M.-R. / Song, H.K.
CitationJournal: Plant Cell / Year: 2011
Title: Single cystathionine beta-synthase domain-containing proteins modulate development by regulating the thioredoxin system in Arabidopsis
Authors: Yoo, K.S. / Ok, S.H. / Jeong, B.-C. / Jung, K.W. / Cui, M.H. / Hyoung, S. / Lee, M.-R. / Song, H.K. / Shin, J.S.
History
DepositionJun 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBS domain-containing protein CBSX2
B: CBS domain-containing protein CBSX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,19810
Polymers39,6922
Non-polymers5058
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-28 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.045, 73.045, 253.453
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 77:131 or resseq 155:231 ) and (not element H)A77 - 131
121chain A and (resseq 77:131 or resseq 155:231 ) and (not element H)A155 - 231
211chain B and (resseq 77:131 or resseq 155:231 ) and (not element H)B77 - 131
221chain B and (resseq 77:131 or resseq 155:231 ) and (not element H)B155 - 231

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Components

#1: Protein CBS domain-containing protein CBSX2 / CBS domain-containing protein 1 / AtCDCP1


Mass: 19846.062 Da / Num. of mol.: 2 / Fragment: resideus in UNP 76-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CBSX2 / Plasmid: pET-GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9C5D0
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris, 0.2M Calcium acetate, 22% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A10.97888, 0.97928, 0.95000
SYNCHROTRONPAL/PLS 6B21.23985
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 1, 2008
ADSC QUANTUM 2102CCDFeb 6, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
20.979281
30.951
41.239851
ReflectionResolution: 1.905→50 Å / Num. obs: 31938 / Redundancy: 25 % / Rsym value: 0.057

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: dev_589)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.905→35.13 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7861 / SU ML: 0.23 / σ(F): 0 / Phase error: 26.73 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1862 6.24 %RANDOM
Rwork0.223 ---
all0.2244 ---
obs0.2244 29856 92.05 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.292 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 130.67 Å2 / Biso mean: 43.3883 Å2 / Biso min: 3.12 Å2
Baniso -1Baniso -2Baniso -3
1-7.5439 Å20 Å2-0 Å2
2--7.5439 Å2-0 Å2
3----10.8814 Å2
Refinement stepCycle: LAST / Resolution: 1.905→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 34 207 2424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072223
X-RAY DIFFRACTIONf_angle_d1.1533009
X-RAY DIFFRACTIONf_chiral_restr0.106370
X-RAY DIFFRACTIONf_plane_restr0.004380
X-RAY DIFFRACTIONf_dihedral_angle_d12.044818
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1033X-RAY DIFFRACTIONPOSITIONAL0.069
12B1033X-RAY DIFFRACTIONPOSITIONAL0.069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9051-1.97320.37171370.322055219269
1.9732-2.05220.34741680.27882622279089
2.0522-2.14560.29161830.2522734291791
2.1456-2.25870.28731880.23512799298795
2.2587-2.40020.26271820.24252695287790
2.4002-2.58540.28171870.24132803299093
2.5854-2.84550.27121930.24222882307595
2.8455-3.2570.26861980.23112983318198
3.257-4.10250.21262080.204730973305100
4.1025-35.13570.20652180.197833243542100
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)
10.8419-1.2569-0.98122.99291.44841.52440.25370.42160.2124-0.1228-0.0662-0.362-0.074-0.0592-0.14430.1429-0.04160.0240.36590.01720.220431.175433.330796.4978
24.81150.6643-0.78224.27071.11572.12-0.04190.5632-0.0765-0.3436-0.1606-0.187-0.37040.41190.18920.264-0.05570.00570.33860.08330.228937.303540.6523105.0692
34.7706-4.65974.18796.2645-4.95345.0932-0.0303-0.68840.3124-0.16990.1339-0.5103-0.0579-0.5702-0.10610.187-0.01170.06130.2738-0.02070.220640.010841.003114.7308
45.98133.7661-0.00682.5599-0.38880.78020.148-0.4863-0.09950.0660.0177-0.1227-0.16350.4595-0.21290.1816-0.0412-0.02150.4325-0.11750.193544.203638.6418126.3752
53.58450.6162.15721.4476-0.37261.71180.0055-0.56950.52160.01780.06660.1795-0.0128-0.6346-0.03840.2608-0.05750.06190.5824-0.09660.281236.259242.3228124.7088
62.6301-1.00520.9083.22710.78410.8666-0.1893-0.9254-0.06980.24840.3264-0.1526-0.03780.3149-0.12480.17630.01870.04020.3666-0.05090.276331.426942.0151119.5747
71.07921.2276-0.11921.6423-0.10410.15430.0074-0.0114-0.2817-0.10240.0698-0.1603-0.21780.16-0.0760.2038-0.110.02640.3504-0.01410.216846.541137.0948115.1283
80.3989-0.57860.37121.0437-0.36920.4745-0.05120.2124-0.1291-0.10340.12910.28020.0353-0.0759-0.07820.0858-0.13740.0140.316-0.01690.19145.505334.2341112.999
90.09210.0842-0.20610.1229-0.08830.6683-0.00280.3110.1214-0.11080.14820.03170.0209-0.2508-0.10090.1535-0.07160.05730.49160.01570.286334.846531.6944125.0304
103.3344-0.08330.3592.9434-3.02713.1365-0.22990.15820.1373-0.1596-0.2427-0.055-0.25030.48710.48570.5260.2613-0.12110.6192-0.04570.213927.651231.3683133.7433
115.14642.2851-4.1463.3084-0.54844.07030.2423-0.33160.03340.0878-0.2883-0.33280.53961.30110.04480.27760.0996-0.05640.5588-0.01830.227728.110837.0366138.4096
123.4517-0.51911.14843.5241-2.26631.65350.0361-1.1697-0.116-0.1019-0.717-0.47030.3030.80120.59460.21010.28560.10810.85670.17160.32435.387835.4972137.8589
134.6547-0.78830.5544.9877-0.69550.1404-0.4954-0.75420.05750.56230.8698-0.0543-0.0793-0.217-0.33740.20770.05970.00330.6724-0.01630.254944.224336.0738131.5014
143.46771.03941.46441.0718-0.24052.28270.0383-0.42170.04580.0733-0.1713-0.00520.04640.16690.15770.1002-0.07340.03980.3811-0.02420.18643.529227.9436120.53
155.49562.6335-1.01294.6557-2.29544.99590.23470.6196-0.15430.08680.0809-0.0520.05880.3125-0.14610.1205-0.0534-0.03110.3567-0.03010.179539.377528.5931102.1445
163.56911.91751.72791.76750.38921.77440.2544-0.159-0.7819-0.05050.0953-0.04230.5196-0.7571-0.290.2844-0.0697-0.01690.3978-0.04020.378629.948824.492103.0026
173.0058-2.2816-0.83172.003-0.8428.2393-0.3505-0.3019-1.4178-0.73940.0898-0.91411.4311-0.41980.2840.5988-0.02460.0880.53660.12030.686831.75925.5618114.6789
180.85660.84860.53831.5617-0.04631.00690.0457-0.0634-0.14240.0115-0.1285-0.1825-0.02370.2210.0959-0.0628-0.14090.11320.38440.01780.163942.536633.213106.4019
190.09740.0790.03790.64220.28260.12560.1371-0.06120.16160.1404-0.09760.2504-0.0474-0.2716-0.14180.139-0.00350.08540.3561-0.01270.23428.18534.344106.2154
205.20634.72743.90776.20312.3346.24880.30130.89481.3433-0.3297-0.53490.21430.0266-0.18920.26050.24140.1310.03790.49510.07010.389620.51835.458497.2607
211.8068-0.51721.59070.3261-0.20421.7556-0.0745-0.4070.24430.0759-0.12150.02420.076-0.45450.18940.37240.12910.07870.3052-0.00490.185122.093849.49133.476
221.38420.055-0.29560.1341-0.25360.52330.16660.39230.0906-0.1525-0.03990.0055-0.5030.0336-0.14660.51840.19890.05350.44090.01520.230918.02950.0939118.6287
230.6628-0.6621-0.67351.10221.34911.7230.11220.17620.0182-0.0668-0.06890.1123-0.4081-0.6470.05120.27630.32760.04230.88420.00360.18627.508142.9447108.6179
243.9490.94943.62794.61433.5095.1154-0.05390.2747-0.0222-0.5914-0.1599-0.0274-0.09540.4470.14910.35970.23620.01380.4834-0.01480.182515.766341.0492105.5226
252.13360.59562.91282.82272.44594.97950.29340.1160.20540.17710.18990.193-0.1349-0.3349-0.41390.26960.09780.10650.45930.08550.123122.982142.3946109.5497
263.91450.0573-1.28940.04370.00611.92250.26940.4051-0.1560.0075-0.19780.0122-0.2598-0.2173-0.03890.18920.2268-0.01950.33280.07110.168815.985740.8804116.0783
270.02070.11120.02830.6815-0.08110.87430.06820.11450.0921-0.2546-0.14050.0985-0.3663-0.40530.02580.49150.74390.00160.80770.07770.25076.202950.4769117.7861
281.26480.57780.07490.4592-0.52181.5771-0.2209-0.0412-0.32580.0786-0.04730.1591-0.0485-0.50050.26770.04860.16010.06620.5391-0.11050.20312.76833.1303113.8037
292.6927-1.13782.77045.43741.23695.09370.06510.8183-1.0760.0976-0.09960.39530.3211-0.33870.0290.2632-0.126-0.02570.5007-0.02060.456421.063124.674103.5885
305.11295.9163-2.9766.8754-3.59442.47870.07170.7431-0.0276-0.31290.07330.85940.0845-0.7326-0.09320.21770.021-0.08430.6541-0.16030.419515.371828.3119100.0708
315.2452-0.35960.05332.05881.66052.6298-0.152-0.9892-0.20040.0438-0.04130.2717-0.2994-0.36990.14410.27350.2851-0.06880.7028-0.03380.2157.332634.3984101.9841
323.9668-2.4458-1.34043.024-0.71932.02960.20970.0491-0.3827-0.2182-0.02320.3630.0231-0.4353-0.17020.13480.3316-0.21180.8920.0110.10335.743936.8003113.8781
333.43120.5572-2.01181.4551-1.05121.56420.16840.9372-0.06850.06690.19060.0845-0.1145-0.4507-0.29230.21630.2311-0.00950.4732-0.05160.16348.323140.347126.7423
340.1998-0.1962-0.3651.7482-0.27370.9304-0.0591-0.03840.0860.13510.2387-0.0521-0.4155-0.2114-0.12950.4090.18410.06020.31310.01810.180214.434348.3612135.46
352.46561.16840.82022.31861.05960.7186-0.1036-0.45580.0697-0.1184-0.1120.0979-0.1618-0.24490.21910.23160.1526-0.00790.4443-0.00090.158918.895739.2657136.7375
360.36390.14420.78680.06140.33741.79550.0910.1512-0.01020.03160.0706-0.24610.10520.1829-0.07720.0240.1417-0.02290.347900.203716.641233.9386126.7534
373.4654-1.8711-0.0872.1831-0.28980.60270.06870.1431-0.2070.0521-0.0470.2736-0.1188-0.05240.0340.18890.24290.04780.36880.01990.215114.641543.503126.0023
380.2354-0.22980.25070.43310.02750.57370.05570.04410.1696-0.1198-0.13190.1672-0.6507-0.7423-0.04910.52230.53960.2580.4714-0.0846-0.03529.958251.2228125.7292
394.1283-2.2447-1.81442.1211-0.59643.58690.34470.4319-0.2990.0661-0.04830.185-0.15470.5163-0.32370.22130.0444-0.00670.359-0.040.236224.651441.2203128.1269
401.38671.0696-0.50963.81692.55093.0818-0.17030.36280.0403-0.10240.3962-0.2575-0.52821.9799-0.24470.3497-0.11760.02430.6623-0.09830.368232.307645.8446133.9412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 76:82)A76 - 82
2X-RAY DIFFRACTION2(chain A and resid 83:87)A83 - 87
3X-RAY DIFFRACTION3(chain A and resid 88:93)A88 - 93
4X-RAY DIFFRACTION4(chain A and resid 94:99)A94 - 99
5X-RAY DIFFRACTION5(chain A and resid 100:106)A100 - 106
6X-RAY DIFFRACTION6(chain A and resid 107:112)A107 - 112
7X-RAY DIFFRACTION7(chain A and resid 113:119)A113 - 119
8X-RAY DIFFRACTION8(chain A and resid 120:125)A120 - 125
9X-RAY DIFFRACTION9(chain A and resid 126:132)A126 - 132
10X-RAY DIFFRACTION10(chain A and resid 133:157)A133 - 157
11X-RAY DIFFRACTION11(chain A and resid 158:162)A158 - 162
12X-RAY DIFFRACTION12(chain A and resid 163:167)A163 - 167
13X-RAY DIFFRACTION13(chain A and resid 168:174)A168 - 174
14X-RAY DIFFRACTION14(chain A and resid 175:181)A175 - 181
15X-RAY DIFFRACTION15(chain A and resid 182:188)A182 - 188
16X-RAY DIFFRACTION16(chain A and resid 189:198)A189 - 198
17X-RAY DIFFRACTION17(chain A and resid 199:203)A199 - 203
18X-RAY DIFFRACTION18(chain A and resid 204:215)A204 - 215
19X-RAY DIFFRACTION19(chain A and resid 216:225)A216 - 225
20X-RAY DIFFRACTION20(chain A and resid 226:231)A226 - 231
21X-RAY DIFFRACTION21(chain B and resid 77:83)B77 - 83
22X-RAY DIFFRACTION22(chain B and resid 84:92)B84 - 92
23X-RAY DIFFRACTION23(chain B and resid 93:98)B93 - 98
24X-RAY DIFFRACTION24(chain B and resid 99:104)B99 - 104
25X-RAY DIFFRACTION25(chain B and resid 105:109)B105 - 109
26X-RAY DIFFRACTION26(chain B and resid 110:115)B110 - 115
27X-RAY DIFFRACTION27(chain B and resid 116:122)B116 - 122
28X-RAY DIFFRACTION28(chain B and resid 123:154)B123 - 154
29X-RAY DIFFRACTION29(chain B and resid 155:161)B155 - 161
30X-RAY DIFFRACTION30(chain B and resid 162:166)B162 - 166
31X-RAY DIFFRACTION31(chain B and resid 167:172)B167 - 172
32X-RAY DIFFRACTION32(chain B and resid 173:178)B173 - 178
33X-RAY DIFFRACTION33(chain B and resid 179:184)B179 - 184
34X-RAY DIFFRACTION34(chain B and resid 185:189)B185 - 189
35X-RAY DIFFRACTION35(chain B and resid 190:196)B190 - 196
36X-RAY DIFFRACTION36(chain B and resid 197:203)B197 - 203
37X-RAY DIFFRACTION37(chain B and resid 204:208)B204 - 208
38X-RAY DIFFRACTION38(chain B and resid 209:217)B209 - 217
39X-RAY DIFFRACTION39(chain B and resid 218:224)B218 - 224
40X-RAY DIFFRACTION40(chain B and resid 225:231)B225 - 231

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