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- PDB-7q3k: Computationally designed thioredoxin subjected to stability optim... -

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Basic information

Entry
Database: PDB / ID: 7q3k
TitleComputationally designed thioredoxin subjected to stability optimizing mutations.
ComponentseMM9
KeywordsDE NOVO PROTEIN / De-novo protein design / Deep mutational scanning / Stability / Screening
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 / _citation_author.name
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: eMM9
B: eMM9
C: eMM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2525
Polymers39,0603
Non-polymers1922
Water00
1
A: eMM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1162
Polymers13,0201
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: eMM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1162
Polymers13,0201
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: eMM9


Theoretical massNumber of molelcules
Total (without water)13,0201
Polymers13,0201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.850, 70.850, 75.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALLEUA1 - 104
d_21ens_1VALLEUD1 - 104
d_31ens_1VALLEUC1 - 104

NCS oper:
IDCodeMatrixVector
1given(0.999993323344, 0.00201447681362, 0.0030487948079), (0.00200352682687, -0.999991547485, 0.00359038141372), (0.00305600177802, -0.00358424909979, -0.999988906944)-0.0125151641586, 41.4520167913, 26.9483795914
2given(-0.365423991336, 0.421674262471, 0.829853073095), (0.847623332035, 0.519191049971, 0.109431899463), (-0.384707672845, 0.743391868397, -0.547145809136)17.0902334169, -8.60222997315, 20.59881198

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Components

#1: Protein eMM9


Mass: 13020.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000 (PEG4000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.25→47.57 Å / Num. obs: 20043 / % possible obs: 99.86 % / Redundancy: 7.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07346 / Rpim(I) all: 0.02929 / Rrim(I) all: 0.07915 / Net I/σ(I): 14.14
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.5328 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1984 / CC1/2: 0.974 / CC star: 0.994 / Rpim(I) all: 0.2148 / Rrim(I) all: 0.575 / % possible all: 99.9

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Processing

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

5j7d


Resolution: 2.25→47.57 Å / Cross valid method: FREE R-VALUE / σ(F): 47.82 / Phase error: 44.2488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3007 1050 5.24 %
Rwork0.2861 18993 -
obs0.3055 20043 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 10 0 2551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01082597
X-RAY DIFFRACTIONf_angle_d1.14333516
X-RAY DIFFRACTIONf_chiral_restr0.0557414
X-RAY DIFFRACTIONf_plane_restr0.0096435
X-RAY DIFFRACTIONf_dihedral_angle_d5.6774330
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.384241000555
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.470182953831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.350.37961800.39612355X-RAY DIFFRACTION92.72
2.35-2.480.43151320.39862307X-RAY DIFFRACTION94.36
2.48-2.630.49071020.40532427X-RAY DIFFRACTION95.66
2.63-2.830.40831120.39922402X-RAY DIFFRACTION95.32
2.84-3.120.3681060.37592407X-RAY DIFFRACTION95.78
3.12-3.570.34631340.33532361X-RAY DIFFRACTION94.63
3.57-4.50.29551380.26892382X-RAY DIFFRACTION94.45
4.5-47.570.25871460.23262352X-RAY DIFFRACTION94.16
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)
10.574432050421-0.04585331062830.08165154838490.370888544117-0.03530136412441.025191101590.01406893833360.08732676061680.112969558557-0.0466204186479-0.0470260258335-0.0257266288011-0.1331047804010.039791703152-0.1441122309430.629143862521-0.1205613804040.1009702505850.601141832491-0.0484013956567-0.3945794926445.119270446811.019764070627.2214162079
20.0257580871672-8.0086902998E-5-0.05121612589780.0006200137623310.02845035839380.05930824198010.0590498020385-0.0596935128560.1344440611130.06652758161330.0076078760915-0.0945604789966-0.04185468971550.09837056160850.3149535348440.641499860409-0.1375290079480.01220496022530.625345776305-0.190327296297-0.7092213817555.9802268275510.798568861319.9786271196
30.1187712709980.04820993323-0.1862520620660.0487857082711-0.04133952714430.3266198927340.00547355853047-0.06084761630210.007254845327940.02303668427090.0407817130355-0.004979557608720.01204456968470.03473290347440.09502477987220.450248507624-0.02237566931140.1094735352940.504181172749-0.05043417760260.0042267154765810.83394654064.1036837241223.4486164671
40.04406559277430.006277488501210.005072546542760.0385051768339-0.04055955536620.04661227600050.0219499591603-0.06094598461-0.008217369846720.0665998582218-0.0195422275843-0.02721590767450.02584613262540.0109698333192-0.04966977041640.5251317306550.0713150161029-0.01651737724480.437469624958-0.0156961108104-0.37522568745210.6653438839-0.24246073433818.4550066973
50.231540009772-0.04726452786450.007836306731260.1712038080060.0390241363130.129366698461-0.01258400722740.00512273781390.02662946846060.0535333551139-0.0172024319510.103656885424-0.0171198533665-0.0114529522088-0.1215655501520.430294104271-0.03644685762410.0006907249254690.6119067989360.121056455454-0.48578508644423.413989197521.6575372119-3.75132214435
60.07882925694030.00835674603518-0.1499901063030.070129257175-0.05710565675470.299965803982-0.03390463468330.0924906291356-0.00857643180107-0.03722923030530.0523983050860.1817765995380.0404276101023-0.1338776014410.2349310488420.450947031727-0.0468866402254-0.08450185763940.6650997768160.0775207092828-0.65915024276223.157906482820.80484033393.44585451881
70.0826678827583-0.0566366867330.0190308162420.1186092782990.08369593831880.1213082335760.003327479081360.00567781286111-0.00909723622936-0.02467270102240.008410928891580.0074479671335-0.07866895324330.03574302743970.1327278464950.530534204193-0.0188001172847-0.06064899005490.5058663392270.06522025138150.060842680721726.719217790313.2931275384-0.170041237511
80.03137785713950.0326886795669-0.03044722104380.0432905191908-0.002641916627150.105268574658-0.03130927624320.0827092111492-0.0296293087404-0.02051496719490.0215074649987-0.01449224014870.05560401499070.0455884686264-0.09034014090460.5484892951910.113181425666-0.05902305062060.5662678785720.00304701308352-0.39074313098630.389271814511.37406701194.74096748978
90.07893911112960.04649004728090.01873223355360.1343968448480.01694853699580.00706427137339-0.000607699342223-0.03980278882990.0285717728913-0.000885968916026-0.00560683462959-0.0314913015174-0.1041281370430.0532472042659-0.0004293303845320.700914211114-0.0357339806990.09749268268150.7362261525940.0278946173630.0804507888295-6.3724046510616.0014745765-1.34392597777
100.0940848624984-0.0178016712508-0.009926600099210.0345762496745-0.04564354069130.0979990432164-0.00380576458981-0.01107423101680.07992451490860.00540742745564-0.0505573257355-0.06329072212970.01915132473830.000504543861084-0.3778053660.596306749244-0.07948647853350.1255682836310.6567261394170.0076199351366-0.391418024908-9.2541387399122.01903921352.06962248376
110.002114184337010.0003796343216940.005319898930150.01932499831060.02883093437450.0545829207520.0193898321348-0.009113047759760.0102682595717-0.006034642486050.002406519360740.003712544670380.000507999380868-0.01191129099040.01924689200870.630070669846-0.05273254362450.1747979974940.768933637360.08077387283120.288356044756-15.526679576918.8261359756-3.68806750601
120.00477258624928-0.00724037179008-0.0180428518080.01026268733980.02361641684730.0573732945929-0.0813179852930.05238353732530.0161381932157-0.00424177046998-0.01692501645540.01690211777670.00594621646418-0.043329023925-0.2601541882860.6626914905250.08291955920920.05891422735330.719967381393-0.001544383857420.0385555673699-21.319863966520.737072071-0.764728199456
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 30 )AA2 - 301 - 29
22chain 'A' and (resid 31 through 74 )AA31 - 7430 - 73
33chain 'A' and (resid 75 through 80 )AA75 - 8074 - 79
44chain 'A' and (resid 81 through 105 )AA81 - 10580 - 104
55chain 'B' and (resid 2 through 30 )BB2 - 301 - 29
66chain 'B' and (resid 31 through 74 )BB31 - 7430 - 73
77chain 'B' and (resid 75 through 80 )BB75 - 8074 - 79
88chain 'B' and (resid 81 through 105 )BB81 - 10580 - 104
99chain 'C' and (resid 2 through 30 )CC2 - 301 - 29
1010chain 'C' and (resid 31 through 74 )CC31 - 7430 - 73
1111chain 'C' and (resid 75 through 80 )CC75 - 8074 - 79
1212chain 'C' and (resid 81 through 105 )CC81 - 10580 - 104

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