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- PDB-6kos: Crystal structure of SUWA (Super WA20), a hyper-stable de novo pr... -

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Basic information

Entry
Database: PDB / ID: 6kos
TitleCrystal structure of SUWA (Super WA20), a hyper-stable de novo protein with a dimeric bisecting topology
ComponentsSUWA (Super WA20)
KeywordsDE NOVO PROTEIN / THERMOSTABLE PROTEIN DESIGN / BINARY PATTERNED DESIGN / FOUR HELIX BUNDLE / 3D DOMAIN SWAPPING / BISECTING U TOPOLOGY
Function / homologyDesigned four-helix bundle protein / hypothetical protein mp506/mpn330, domain 1 / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKimura, N. / Arai, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP24113707, JP24780097, JP16K05841, JP16H00761, JP17KK0104, JP19H02522 Japan
Citation
Journal: Acs Synth Biol / Year: 2020
Title: HyperstableDe NovoProtein with a Dimeric Bisecting Topology.
Authors: Kimura, N. / Mochizuki, K. / Umezawa, K. / Hecht, M.H. / Arai, R.
#1: Journal: J Phys Chem B / Year: 2012
Title: Domain-swapped dimeric structure of a stable and functional de novo four-helix bundle protein, WA20.
Authors: Arai, R. / Kobayashi, N. / Kimura, A. / Sato, T. / Matsuo, K. / Wang, A.F. / Platt, J.M. / Bradley, L.H. / Hecht, M.H.
History
DepositionAug 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUWA (Super WA20)
B: SUWA (Super WA20)
C: SUWA (Super WA20)
D: SUWA (Super WA20)


Theoretical massNumber of molelcules
Total (without water)50,1694
Polymers50,1694
Non-polymers00
Water2,468137
1
A: SUWA (Super WA20)
B: SUWA (Super WA20)


Theoretical massNumber of molelcules
Total (without water)25,0852
Polymers25,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-80 kcal/mol
Surface area11270 Å2
MethodPISA
2
C: SUWA (Super WA20)
D: SUWA (Super WA20)


Theoretical massNumber of molelcules
Total (without water)25,0852
Polymers25,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-80 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.636, 71.930, 81.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SUWA (Super WA20)


Mass: 12542.261 Da / Num. of mol.: 4 / Mutation: H26L, G28S, N34L, V71L, E78L
Source method: isolated from a genetically manipulated source
Details: Hyper-stable de novo protein SUWA (Super WA20) / Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.92 Å3/Da / Density % sol: 35.9 % / Description: Rod-like
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2016 / Details: Collimating Mirror-Monochromator-Focusing Mirror
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 26639 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Χ2: 0.998 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.077.10.6292.7726130.8670.2520.6790.997100
2.07-2.157.20.3984.3726150.9370.1580.4291100
2.15-2.257.20.2896.1626590.9640.1150.3121.006100
2.25-2.377.30.1998.7326330.9830.0790.2140.98799.8
2.37-2.527.30.13513.226200.9920.0530.1451.01999.8
2.52-2.717.20.09318.826710.9960.0370.11.01199.9
2.71-2.997.20.06426.526650.9980.0250.0690.97799.9
2.99-3.427.20.04834.626790.9990.0190.0520.989100
3.42-4.3170.03745.627100.9990.0150.040.997100
4.31-506.70.02177.7277410.0090.0220.99396.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VJF
Resolution: 2→31.23 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / Matrix type: sparse / WRfactor Rfree: 0.31 / WRfactor Rwork: 0.241 / SU B: 11.752 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2837 1358 5.1 %RANDOM
Rwork0.223 25230 --
obs0.226 25230 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.79 Å2 / Biso mean: 48.908 Å2 / Biso min: 25.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2---1.25 Å20 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 2→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 0 137 3499
Biso mean---49.86 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133464
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172969
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.6144646
X-RAY DIFFRACTIONr_angle_other_deg1.4591.5746983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9155393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.46326.026234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8715685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.643154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.0530.334950.2751856X-RAY DIFFRACTION99.693
2.053-2.1090.2661000.2431779X-RAY DIFFRACTION100
2.109-2.170.2881010.2391733X-RAY DIFFRACTION100
2.17-2.2370.277990.2311695X-RAY DIFFRACTION100
2.237-2.310.253950.2321636X-RAY DIFFRACTION99.769
2.31-2.3910.3830.2191597X-RAY DIFFRACTION100
2.391-2.4810.259850.2381535X-RAY DIFFRACTION99.754
2.481-2.5820.325810.2311502X-RAY DIFFRACTION100
2.582-2.6960.283890.2381402X-RAY DIFFRACTION99.799
2.696-2.8280.269670.2251375X-RAY DIFFRACTION100
2.828-2.980.294600.2211311X-RAY DIFFRACTION99.782
2.98-3.160.278760.2241237X-RAY DIFFRACTION100
3.16-3.3770.298650.211168X-RAY DIFFRACTION100
3.377-3.6460.275470.2071103X-RAY DIFFRACTION100
3.646-3.9920.233420.2141016X-RAY DIFFRACTION100
3.992-4.460.291510.207925X-RAY DIFFRACTION100
4.46-5.1430.281400.199834X-RAY DIFFRACTION99.658
5.143-6.2820.394370.266701X-RAY DIFFRACTION100
6.282-8.8150.271350.229557X-RAY DIFFRACTION99.329
8.815-31.230.229100.239268X-RAY DIFFRACTION76.164
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)
135.837719.4329-2.874532.6298-7.95062.0923-0.62140.4236-0.88490.46270.4506-0.9557-0.0869-0.11810.17080.76250.0013-0.11050.3891-0.00340.2598-8.7698-30.273-41.5026
27.20347.78271.851918.07487.42885.8089-0.09070.0497-0.7742-0.22770.238-1.00670.52470.3848-0.14740.39550.07260.00340.2377-0.03940.3353-4.2775-17.2683-39.2758
30.1285-0.07891.182319.15632.98512.34770.01010.0196-0.01580.27150.1579-0.79730.35570.6213-0.1680.21850.0261-0.01450.299-0.0330.2709-3.3149-3.8476-36.0415
44.52412.14252.499323.8231.15565.78980.00020.3169-0.0417-0.53840.2463-0.5320.05920.3782-0.24650.218-0.00520.00730.3005-0.00630.2726-2.5936.4211-34.6315
57.33161.20281.740131.9019-2.11474.58470.06390.0306-0.1194-0.20120.080.0245-0.09940.2541-0.14390.2394-0.02160.0360.2458-0.01050.2537-4.011316.8684-34.4733
67.70561.3828-1.308422.64211.79514.0173-0.09020.38140.3233-0.62580.0707-0.4498-0.35840.19810.01950.3391-0.0450.05220.292-0.03410.264-3.988929.9793-35.8385
70.0001-0.0033-0.00020.15580.02730.007-0.03120.00320.0057-0.35080.0765-0.1341-0.06050.0578-0.04530.8059-0.18480.21510.9498-0.17390.7973-0.956837.4642-44.3475
810.47661.288-19.04613.762.888136.63950.798-0.03130.3995-0.91620.1767-0.9223-1.68750.074-0.97460.6341-0.28460.04760.3413-0.08560.8527-1.567330.0213-46.4152
912.18569.24880.212919.4191-1.95669.8569-0.17960.27210.3838-0.57910.2455-0.5311-0.60910.6997-0.06590.345800.080.332-0.0740.2841-5.589318.4763-47.1392
103.10145.91370.172417.85651.72450.3615-0.05460.00880.2107-0.34770.17920.2522-0.0564-0.0376-0.12460.28170.0517-0.05030.3050.01140.2566-15.01121.4321-44.2454
117.5355-0.12260.660925.6794-8.58086.3914-0.266-0.27750.01190.11550.26990.58240.1245-0.4888-0.00390.28520.0211-0.01260.3189-0.00660.2315-22.4251-14.3925-41.5106
1235.230217.8712-26.429630.5801-1.663526.2388-0.4879-0.8744-0.6045-0.8746-1.29361.95810.15440.11991.78160.3770.0482-0.24770.50710.13070.8428-27.1981-25.0952-38.4399
135.85461.61354.850432.7256-5.285919.6249-0.76110.47810.83621.91760.7277-1.4152-0.22941.49130.03340.4592-0.047-0.08920.4585-0.09150.61186.085822.3397-38.5449
147.337810.2087-4.009827.70254.60769.9449-0.0073-0.14160.04120.08250.4128-0.70960.04390.5871-0.40550.352-0.0854-0.03560.58540.01740.58552.968612.5575-42.1553
1519.042611.10138.455929.87510.64877.37490.10790.89380.4847-0.407-0.05090.3692-0.41940.8556-0.0570.4456-0.05480.17150.3816-0.0990.2478-2.1474.2777-44.2203
1611.70776.06330.589112.5991.24759.3468-0.0880.5190.5575-0.57550.4286-0.3219-0.60910.4742-0.34060.2735-0.01530.01970.2968-0.0250.2138-5.7634-4.527-45.7784
177.30998.69320.864818.54961.0861.3382-0.27370.40830.2002-0.38820.33150.20840.0713-0.023-0.05790.311-0.0104-0.01340.29240.00130.1895-14.5436-19.4768-45.79
188.28371.2512-9.344430.299312.875520.07170.2410.2337-0.31250.1334-0.44650.6930.4583-0.91670.20550.3043-0.0432-0.06340.27950.15180.2467-19.1449-31.5613-46.5614
1932.223721.187316.515722.681314.412222.4338-0.17690.6413-3.072-0.0471-0.30820.14790.9059-1.19310.48510.6009-0.0477-0.00970.4983-0.13851.1566-19.6173-34.9367-38.3868
201.9551-1.02520.642119.70885.462115.10580.08290.0518-0.31410.56680.02470.34020.5916-0.3637-0.10760.333-0.0378-0.0210.23240.11950.2653-16.3188-26.3487-34.6483
213.70030.59370.375923.50531.64682.5252-0.0408-0.452-0.14660.68550.17340.5160.1394-0.1881-0.13260.29980.00830.02080.28940.02610.1912-15.7285-10.3786-33.2556
222.7824.4503-3.395616.6636-6.92517.4867-0.02910.06890.2270.21320.26191.0291-0.2404-0.6145-0.23280.21850.0563-0.00940.3283-0.03980.2881-14.86797.637-35.5405
238.48150.7211-1.010222.529-7.16247.8320.0974-0.3136-0.18640.26280.19420.7088-0.5261-0.2644-0.29150.26740.0070.03770.2479-0.02260.2858-13.449218.798-38.5031
243.797-5.05554.732918.8093-11.396517.78220.17750.43830.3588-0.2673-0.02530.9276-0.9515-0.5051-0.15220.60960.01830.07250.4005-0.00680.3966-11.916327.7847-42.9187
2514.8251-12.216-20.326836.295211.299729.5317-0.0017-0.88550.6367-0.6582-0.2619-1.98490.35321.9720.26360.1298-0.13820.09290.93310.42691.158539.7834-3.0744-21.3201
2624.146-11.4456-6.26868.06954.60376.01640.3064-0.73620.98080.00060.0078-0.8612-0.44810.8708-0.31420.3048-0.139-0.06240.3652-0.0210.391127.79510.6248-16.4059
2719.1194-3.4358-1.81861.87470.17751.9951-0.13220.03210.1160.10590.0527-0.0475-0.35730.03470.07950.3020.0059-0.02510.2155-0.06540.24639.04943.1249-13.3691
2831.17072.40882.84812.4603-2.662713.38570.3489-0.3565-0.14780.6781-0.2434-0.21120.2869-0.1063-0.10560.28570.03240.01840.2449-0.05080.1954-5.10224.9577-12.008
2910.1041-7.0467-3.582310.4025-0.413513.14540.00270.1059-0.2401-0.32160.15370.50420.1914-0.167-0.15640.2528-0.02090.03420.2516-0.00920.2561-15.54995.4325-13.3511
3055.095112.966324.94463.13655.88711.29950.0854-3.98870.7029-0.1401-0.64080.4232-0.0747-1.82160.55550.6747-0.05-0.12920.9520.31580.8868-24.27117.7963-19.0158
3123.9462-14.1455-2.269325.64661.51654.31640.20840.6870.2716-0.908-0.66850.681-0.4233-0.55790.46010.39290.034-0.03880.2592-0.04080.2146-16.57211.0743-23.7846
3214.1268-4.76550.37772.7137-0.36975.0365-0.0323-0.1518-0.00150.27890.06270.0809-0.1748-0.1185-0.03050.28670.00680.00290.2314-0.02640.2376-6.53235.7771-25.7557
3315.0099-9.2586-0.595611.601-1.73560.77980.0203-0.0198-0.23420.09420.06790.4024-0.02080.0177-0.08820.25790.017-0.0230.2732-0.04080.18923.1326-0.5294-24.9492
3421.5159-8.46994.682310.18492.056411.04270.1640.45750.0452-0.3245-0.1583-0.1136-0.3808-0.1461-0.00570.2534-0.0136-0.00620.2333-0.02080.216110.6436-5.3252-24.6495
357.9923-7.85836.486112.75-7.50435.52950.31880.3283-0.0865-0.4977-0.4169-0.36580.2960.27790.09810.2488-0.02350.00190.2529-0.03720.281619.6399-12.2241-24.4817
3633.6474-23.9896.48521.1755-0.03926.48370.77261.5093-0.2584-0.3215-0.524-0.17480.47871.0082-0.24860.29060.16510.22350.41170.16310.576630.8529-20.7735-23.0082
378.41380.9645-8.15810.06845.342611.86920.22250.29210.24540.1115-0.07250.1306-0.1328-0.3426-0.14990.37780.10340.02940.26570.06830.3063-14.711515.3557-14.5095
3822.0686-8.2616-6.80656.12692.54732.26110.35960.28420.9908-0.1392-0.0924-0.2678-0.35430.0441-0.26720.4735-0.0494-0.0460.3271-0.00910.2373-0.948512.7066-18.4715
3926.3202-15.0395-4.27628.67463.301712.93650.05230.72430.1327-0.1371-0.3452-0.0115-0.51360.53780.29290.3466-0.0199-0.04440.40120.09070.236912.18415.7568-23.0508
4012.4117-5.8016-5.043310.89632.94628.04850.11480.37650.0903-0.2376-0.2394-0.1642-0.1942-0.33980.12460.2418-0.0443-0.01590.33310.02190.2821.5076-1.3191-24.5351
4123.4536-15.8309-4.153620.69941.208713.3552-0.08470.60690.3759-0.8674-0.304-0.38310.38490.68050.38870.2479-0.05610.09010.36370.12260.351331.4243-7.7839-26.4635
4220.547-23.1126-2.337635.7938-12.820524.6469-0.1830.0569-0.6160.33890.05530.5024-0.5803-0.56060.12760.28070.01180.09260.49610.18460.387138.5832-12.214-27.3115
430.97210.20954.30370.0540.948419.19030.13740.1615-0.17860.02180.2778-0.0562-0.05530.9396-0.41520.46630.0538-0.00460.8245-0.08570.790344.8025-15.9739-19.8072
4446.1282.1017-0.72277.3606-0.95112.3771-0.67070.41260.3945-0.051-0.0331-0.3998-0.06140.48220.70370.33920.0283-0.03550.52350.13090.537535.6345-14.0474-14.5649
4520.2841-9.89221.23145.1005-0.80560.269-0.6347-0.92740.58290.61240.4929-0.3659-0.20930.03840.14180.50210.073-0.09720.3762-0.02190.301820.7191-10.4662-14.5721
4618.0561-3.00524.11713.3345-2.98232.80920.0046-0.2506-0.3047-0.29110.14920.19010.2845-0.1502-0.15380.3278-0.01620.05950.1952-0.03430.27874.0339-7.0898-15.3416
4745.91765.08344.090610.05370.54930.37460.3567-0.0269-0.0818-0.3246-0.38030.15730.08880.00130.02360.468-0.00230.04040.24260.03570.2972-4.8441-4.1686-18.18
4813.6165-5.87814.30397.1756-0.93497.0010.46960.8524-0.4509-0.9748-0.5910.86450.2955-0.09090.12140.60510.0096-0.10140.24870.02030.4391-14.162-2.4602-21.2226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2A7 - 17
3X-RAY DIFFRACTION3A18 - 24
4X-RAY DIFFRACTION4A25 - 32
5X-RAY DIFFRACTION5A33 - 38
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