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- PDB-8wx8: De novo design protein -T09 -

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Basic information

Entry
Database: PDB / ID: 8wx8
TitleDe novo design protein -T09
ComponentsDe novo design protein -T09
KeywordsDE NOVO PROTEIN / De novo design protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, C. / Wang, S. / Liu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Methods / Year: 2024
Title: De novo protein design with a denoising diffusion network independent of pretrained structure prediction models.
Authors: Liu, Y. / Wang, S. / Dong, J. / Chen, L. / Wang, X. / Wang, L. / Li, F. / Wang, C. / Zhang, J. / Wang, Y. / Wei, S. / Chen, Q. / Liu, H.
History
DepositionOct 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: De novo design protein -T09
B: De novo design protein -T09


Theoretical massNumber of molelcules
Total (without water)52,5012
Polymers52,5012
Non-polymers00
Water1,22568
1
A: De novo design protein -T09


Theoretical massNumber of molelcules
Total (without water)26,2501
Polymers26,2501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo design protein -T09


Theoretical massNumber of molelcules
Total (without water)26,2501
Polymers26,2501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.026, 59.415, 85.421
Angle α, β, γ (deg.)90.000, 94.830, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein De novo design protein -T09


Mass: 26250.498 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M Imidazole malate pH5.5 33% w/v PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→29.71 Å / Num. obs: 20206 / % possible obs: 97.96 % / Redundancy: 6.8 % / Biso Wilson estimate: 42.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1088 / Net I/σ(I): 15.89
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 1979 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.71 Å / SU ML: 0.3187 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4143
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2517 938 4.65 %
Rwork0.2119 19245 -
obs0.2138 20183 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 0 68 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283318
X-RAY DIFFRACTIONf_angle_d0.53724530
X-RAY DIFFRACTIONf_chiral_restr0.0438605
X-RAY DIFFRACTIONf_plane_restr0.0033571
X-RAY DIFFRACTIONf_dihedral_angle_d16.61841154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.34161330.28282717X-RAY DIFFRACTION97.4
2.42-2.570.33771450.26072697X-RAY DIFFRACTION97.6
2.57-2.770.29451260.26572719X-RAY DIFFRACTION97.77
2.77-3.050.30791240.23152766X-RAY DIFFRACTION98.07
3.05-3.490.31021290.21482751X-RAY DIFFRACTION98.56
3.49-4.40.19641530.19132758X-RAY DIFFRACTION98.41
4.4-29.710.22071280.18832837X-RAY DIFFRACTION98.15
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)
15.806121251-1.54864291108-0.4133933818065.06842518664-1.215928796346.369364414290.155804132818-0.3806494134630.3216346154771.00738188262-0.275085751303-0.389018071986-0.4135485604680.7440124653850.1305393479630.661248855981-0.104474754553-0.1541162367750.3057800707690.02550472810060.3857090702767.31499550079-12.730988756250.527212306
26.895563291660.417835695355-1.997438030245.698071331180.2174022813147.443679071060.2301583245010.561407108239-0.160965463082-0.330990982734-0.489829734761-1.148757686770.3263917251591.605913689090.4027393386790.3660215421290.0706285230331-0.01105785058530.5934318741120.08476091866560.53633423612516.1663731218-20.944772581837.7620891999
38.48979707796-1.487654283541.749201152119.78396633244-5.777934614778.60221116811-0.709085045120.315344845743-0.211137928066-1.151292165920.257002043299-1.763115754330.1803863335480.4412231008310.5819478036580.367825657418-0.01005104458690.08588862474290.326252107346-0.04573605329270.24316621928.00398676559-13.220962533431.3673361769
44.49142400987-4.243375963680.628133205237.54249128808-0.2504337992974.310617900360.8592991686971.06546751060.682253952353-1.44519754141-0.961652788684-0.819334188458-0.2573328571980.7630479734110.1655094655530.6282827141830.05123995155850.05910198235480.6049603758220.1493483198540.4500180689976.09572708047-10.43896309726.6149915743
56.49144725676-3.19269039548-0.1271740363312.613911755611.95430800036.979870705390.12659925764-0.1690749413760.02893815950430.263731396371-0.275325079852-0.250187826468-0.0541466138421-0.180849037410.2012472375090.310229029907-0.0140710339694-0.02833066848770.2509589951230.01860201006940.234174954915-0.732906264416-6.1246449885929.433330355
63.52761835497-4.29523442491-0.4479770887083.014548721750.2495194740556.231974989860.09876184832-0.079538441373-0.05921300442340.186760645397-0.1934990089250.193835939466-0.250783473936-0.2346490902780.1342829865430.339882355294-0.0387975152016-0.01454899362010.253243611986-0.04795239191360.294522329893-6.91781733038-4.0254706430134.3450533933
72.424065958133.889717669387.615874318523.945013008143.388722036867.499322409690.660384288034-0.281653135382-0.25458953320.606681957734-0.4694978611560.3288648861850.235119175654-0.486116659016-0.2952481980830.586253060001-0.0001543344775880.02728026402410.295425742876-0.05697777552880.449808845378-12.08419418940.43313861308142.0931428755
85.16328350772-5.220601051210.6173885333655.47692249678-2.23011234018.48427254536-0.238098727535-0.1690345585850.7018210646180.8283232241160.05423693562140.0964280785621-0.5167587396190.152419389260.1817684907480.732020679145-0.04932463645230.01197336183660.228159337617-0.02091684285660.530454969298-3.40956900572-3.5094420623249.898686127
98.059539304041.223016037262.367175215626.47620079920.5855194813419.23535286363-0.3122112290720.9573151694070.640688466742-1.757183507350.0443874064095-0.1163127385350.8369596796750.1077001017630.1187369152251.198714336920.0850170715737-0.1074341538340.3980437765890.01986136200110.445343739419-20.0505096979-14.1670070366-13.2952510714
106.65638538530.9240450754611.276591099476.525709619170.746652554615.827405834130.2073928856520.467060602903-0.0862188357612-1.31662706241-0.293888677803-0.5642585664590.2045016878650.8826611722330.1326565686990.7062419917030.1323290968310.07896596071050.3639814307510.09088515804650.433622251477-9.25710933867-6.68417083606-7.72068468909
119.08508436878-1.151000930790.8246235453988.68788984874-2.079197913586.698584473590.269982314539-0.6248736087820.3232128718081.38672757031-0.334200186702-1.086526757030.1371695775281.202527181470.03471112767230.624400307889-0.0491635744313-0.1807992313960.6071363453040.02627525538030.400124129189-4.59466509805-6.596994693166.58687129625
122.21193320612-0.7279230337460.4610346047487.88252557619-3.674670446192.138264664920.1480934783120.2125927980120.407010664368-1.324908529050.00164998934908-0.904001845241-0.1389072342591.45010605191-0.2596814727690.939568493497-0.0467450458951-0.2664204208830.713578998924-0.0655469761990.526778437338-3.62156741014-12.197270131615.2855379036
132.805516608867.26007061030.6308125075592.251876329332.548199985445.124797387330.273941254602-0.086839444776-0.2692751870550.295970633794-0.2937793520180.406626735577-0.0242512766649-0.1029432405150.1534445836160.614961660180.0874966116584-0.1272063325820.3861570765020.03420233729580.542169392237-12.3061669713-14.92443965328.90626472347
147.83832131045.333331026173.629093881218.190915247890.5699021181598.282274067020.727847478374-0.315368476336-0.612935823771.15590587093-0.181485008997-0.8182693886360.2573800378120.0524960504728-0.3855726634590.569986409123-0.0186457791887-0.1677394305740.335568266935-0.004511662383870.368906137989-16.4446866802-17.93850792611.5783405675
155.573849644633.840999517611.605809536825.61062625248-0.1261531787783.108468178340.0714014111277-0.3213206595930.35102620780.0820186921149-0.2407628088070.464176595436-0.247260019812-0.3014306320920.1983318628610.5099242933190.0456206610208-0.03486804618760.277907742796-0.03116229983350.299401007564-26.0227480622-21.27652784476.53010570683
166.959757415083.633211906372.407000071183.80390901805-0.4229435538276.8441805942-0.5396200467840.1742362222830.472936332798-1.140982592320.0653915744351.307947440510.1435506622410.01308825822650.4266605567720.9665924404790.0443513492013-0.2260854501840.343218106493-0.05448365110340.702004289066-25.4021675848-19.8081005543-6.42412666407
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 65 )AA1 - 651 - 65
22chain 'A' and (resid 66 through 101 )AA66 - 10166 - 101
33chain 'A' and (resid 102 through 115 )AA102 - 115102 - 115
44chain 'A' and (resid 116 through 139 )AA116 - 139116 - 139
55chain 'A' and (resid 140 through 162 )AA140 - 162140 - 162
66chain 'A' and (resid 163 through 189 )AA163 - 189163 - 189
77chain 'A' and (resid 190 through 203 )AA190 - 203190 - 203
88chain 'A' and (resid 204 through 229 )AA204 - 229204 - 227
99chain 'B' and (resid 1 through 26 )BB1 - 261 - 26
1010chain 'B' and (resid 27 through 90 )BB27 - 9027 - 90
1111chain 'B' and (resid 91 through 115 )BB91 - 11591 - 115
1212chain 'B' and (resid 116 through 127 )BB116 - 127116 - 127
1313chain 'B' and (resid 128 through 139 )BB128 - 139128 - 139
1414chain 'B' and (resid 140 through 162 )BB140 - 162140 - 162
1515chain 'B' and (resid 163 through 203 )BB163 - 203163 - 203
1616chain 'B' and (resid 204 through 229 )BB204 - 229204 - 228

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