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- PDB-7q3j: Computationally designed thioredoxin subjected to stability optim... -

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Basic information

Entry
Database: PDB / ID: 7q3j
TitleComputationally designed thioredoxin subjected to stability optimizing mutations.
ComponentsMM9
KeywordsDE NOVO PROTEIN / De-novo protein design / Deep mutational scanning / Stability / Screening
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNorrild, R.K. / Johansson, K.E. / O'Shea, C. / Lindorff-Larsen, K. / Winther, J.R. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research Denmark
CitationJournal: Cell Rep Methods / Year: 2022
Title: Increasing protein stability by inferring substitution effects from high-throughput experiments.
Authors: Norrild, R.K. / Johansson, K.E. / O'Shea, C. / Morth, J.P. / Lindorff-Larsen, K. / Winther, J.R.
History
DepositionOct 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MM9
B: MM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9394
Polymers26,7552
Non-polymers1842
Water1,35175
1
A: MM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4702
Polymers13,3771
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4702
Polymers13,3771
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.890, 45.656, 72.882
Angle α, β, γ (deg.)90.000, 92.155, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21B-327-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 18 through 30 or resid 32...
d_2ens_1(chain "B" and (resid 18 through 30 or resid 32...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUGLUA1 - 13
d_12ens_1ALAVALA15 - 18
d_13ens_1TYRVALA20 - 22
d_14ens_1GLUALAA24 - 26
d_15ens_1GLUGLYA28 - 88
d_21ens_1LEUGLUD1 - 13
d_22ens_1ALAVALD15 - 18
d_23ens_1TYRVALD20 - 22
d_24ens_1GLUALAD24 - 26
d_25ens_1GLUGLYD28 - 88

NCS oper: (Code: givenMatrix: (0.999936094174, 0.00722526175212, -0.00869500780192), (0.00735945100248, -0.999852765349, 0.0155011646368), (-0.00858172762352, -0.0155641645059, -0.999842042892)Vector: ...NCS oper: (Code: given
Matrix: (0.999936094174, 0.00722526175212, -0.00869500780192), (0.00735945100248, -0.999852765349, 0.0155011646368), (-0.00858172762352, -0.0155641645059, -0.999842042892)
Vector: -1.45142365654, -1.35876407848, 36.7430322023)

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Components

#1: Protein MM9


Mass: 13377.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M NaOAc, 0.1 M Tris-HCl (pH 8.5), 30 % polyethylene glycol 4000 (PEG4000).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→25.93 Å / Num. obs: 14904 / % possible obs: 96.53 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.66 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.06275 / Rpim(I) all: 0.03932 / Rrim(I) all: 0.07447 / Net I/σ(I): 22.28
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3193 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 1490 / CC1/2: 0.755 / CC star: 0.928 / Rpim(I) all: 0.193 / Rrim(I) all: 0.3746 / % possible all: 95.69

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j7d

5j7d


Resolution: 1.9→25.93 Å / SU ML: 0.2254 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 27.9138
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 759 5.1 %
Rwork0.192 14134 -
obs0.1945 14893 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 12 75 1523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01241482
X-RAY DIFFRACTIONf_angle_d1.15411997
X-RAY DIFFRACTIONf_chiral_restr0.0623227
X-RAY DIFFRACTIONf_plane_restr0.0115253
X-RAY DIFFRACTIONf_dihedral_angle_d25.3359561
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.483151800215 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.27191440.24052801X-RAY DIFFRACTION96.53
2.05-2.250.28371510.21732833X-RAY DIFFRACTION97.42
2.25-2.580.27361420.2092851X-RAY DIFFRACTION97.33
2.58-3.250.2421540.20642880X-RAY DIFFRACTION98.38
3.25-25.930.21541680.16722769X-RAY DIFFRACTION93.36
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.910359218423-0.3336269180360.5789295008440.52044195248-0.2347255567180.493211800712-0.113825914758-0.57458648111-0.04079719638830.1986668394190.348735555372-0.7159067112020.257276903040.6505259981370.002808064718140.2164362600820.04686381380910.01477597653780.241822939435-0.03134070321460.29829859211811.194832988910.09813186075.15037068646
20.203855599292-0.0120281957440.1998819476760.05341958480610.05528223737560.273592439630.4378703837040.2477773791140.5007982838631.221163809460.05291742939550.481461322341-0.5936540859860.1425457557250.05346399045180.9150290217360.3433994638680.1864938252191.062430815030.1234498971020.9317100265964.8646960707610.714346533821.0937693016
30.8641081754720.6079753443580.3362466783151.15780602294-0.2100455949881.31878437584-0.0544534056666-0.943272066045-0.2315956548550.6088788802910.0500179162474-0.142278858085-0.4217333465270.3919969159190.0009613022090270.5140024003650.08162783417940.03622365877140.4449859717460.08178490113390.27344962213612.11231533722.1714207422712.7624587537
40.6971416314-0.3091038661860.5646445950270.553733646041-0.4806516408340.930026108486-0.209919294824-0.4463106374850.3352768839860.05685552276230.277537050106-0.507540110037-0.09572504133950.3501667890790.00105603224820.2169696160530.0414800997873-0.03900791387350.300577110482-0.04459849890320.33739563824116.35006658698.372671729415.02801157004
50.408557213499-0.03276157723820.09075929431680.924091027116-0.8305586338270.766089456656-0.316166000723-0.6479381011890.5131621143420.3364914203230.556053886449-0.33222137365-0.675484471063-0.03801930780960.08440939155170.3023524228270.0254661310785-0.06977139487650.438791309365-0.1158197687190.3382821092695.3388494527521.52903664099.28606517796
64.04701827485-1.185915029931.54456309213.648008510790.2858164179970.920935191799-0.131712448347-0.267631595506-0.1615151382970.1286347377060.04967063779740.31000087075-0.0533770630166-0.1430995176860.0007049803204540.201647257880.002390512851510.01777353842890.2775061892850.01951316328540.2293550603294.029771666119.681184142862.77849549848
70.7361371152350.166835328739-0.3093237966450.4120740888510.4341623580940.798337072647-0.264269060701-0.126894491597-0.9824349048120.05071589330810.08581340773330.4053445696240.404396007379-0.2642819033520.003564311846190.3579387957960.03265620977170.09062663166430.290300391146-0.04433471586250.4810818557639.16183991627-1.18967595344-0.253743500892
81.37473662838-1.29872982027-0.5237213619052.64203896862-0.08591128233810.777732824312-0.246548011321.11432932072-0.0223865024944-1.084612569130.382856013448-0.511599041261-0.06602163402750.6668187470920.1762406724550.427778661306-0.13814425990.07064938374940.440263021099-0.02960269188390.1517843809497.79720216021-12.078576054226.1085596506
91.878614044140.2535550224770.789428174222.152653613420.5069212911783.58169444848-0.1921832374240.9421128715660.267790311459-0.4604430142350.543078316509-0.02339992418930.1032161081461.008330216050.07484155588050.513564488933-0.119782862238-0.002932545367950.4419536672340.08335647101720.3210328061059.77429111701-3.4946399271322.7784127865
100.6319251491220.2288305768820.04638513517951.00399092745-0.4943024263731.24738039614-0.001111819448250.387403771108-0.411847524079-0.003026627258130.233459802454-0.5700147742460.354838947930.6104103630950.01184753262990.1969687003-0.02090112189110.05694626269770.326091738252-0.07296489940430.28835229371514.9263926827-9.5902303714531.3745629855
111.580182380580.410079490326-0.8664772648450.828427068735-1.029745335841.39326603046-0.4136195681840.812314431718-1.02361427072-0.3082320994340.399316926534-0.05910658630040.9982783683380.01419095689380.07559168479580.478477130706-0.002117749236720.05653390322420.374394452456-0.1420910470160.3466708847213.93888845459-22.797122885827.1160744627
124.305317783511.72375025176-0.4943944724823.439915467071.391696265511.5759643545-0.106982726056-0.008387145494950.344066093977-0.1804577730560.1264710554980.369283553371-0.285990228121-0.1671293111650.0004422699638110.308825411964-0.0292508779003-0.05204693837510.251836671905-0.0006173751355850.2670617154034.4681580925-7.0313798979834.9435220395
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 25 )AA18 - 251 - 8
22chain 'A' and (resid 26 through 30 )AA26 - 309 - 13
33chain 'A' and (resid 31 through 45 )AA31 - 4514 - 28
44chain 'A' and (resid 46 through 56 )AA46 - 5629 - 39
55chain 'A' and (resid 57 through 66 )AA57 - 6640 - 49
66chain 'A' and (resid 67 through 92 )AA67 - 9250 - 75
77chain 'A' and (resid 93 through 105 )AA93 - 10576 - 88
88chain 'B' and (resid 18 through 29 )BD18 - 291 - 12
99chain 'B' and (resid 30 through 45 )BD30 - 4513 - 28
1010chain 'B' and (resid 46 through 56 )BD46 - 5629 - 39
1111chain 'B' and (resid 57 through 66 )BD57 - 6640 - 49
1212chain 'B' and (resid 67 through 105 )BD67 - 10550 - 88

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