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- PDB-6nz1: Crystal structure of computationally designed protein XXA_GVDQ -

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Basic information

Entry
Database: PDB / ID: 6nz1
TitleCrystal structure of computationally designed protein XXA_GVDQ
ComponentsDesign construct XXA_GVDQ
KeywordsDE NOVO PROTEIN / homotrimer / helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWei, K.Y. / Bick, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM124149 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.
Authors: Wei, K.Y. / Moschidi, D. / Bick, M.J. / Nerli, S. / McShan, A.C. / Carter, L.P. / Huang, P.S. / Fletcher, D.A. / Sgourakis, N.G. / Boyken, S.E. / Baker, D.
History
DepositionFeb 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Design construct XXA_GVDQ
B: Design construct XXA_GVDQ
C: Design construct XXA_GVDQ
D: Design construct XXA_GVDQ
E: Design construct XXA_GVDQ
F: Design construct XXA_GVDQ


Theoretical massNumber of molelcules
Total (without water)67,2306
Polymers67,2306
Non-polymers00
Water4,630257
1
A: Design construct XXA_GVDQ
B: Design construct XXA_GVDQ
C: Design construct XXA_GVDQ


Theoretical massNumber of molelcules
Total (without water)33,6153
Polymers33,6153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-91 kcal/mol
Surface area13320 Å2
MethodPISA
2
D: Design construct XXA_GVDQ
E: Design construct XXA_GVDQ
F: Design construct XXA_GVDQ


Theoretical massNumber of molelcules
Total (without water)33,6153
Polymers33,6153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-90 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.647, 76.747, 91.946
Angle α, β, γ (deg.)90.000, 106.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Design construct XXA_GVDQ


Mass: 11204.926 Da / Num. of mol.: 6
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 / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.03 M of each divalent cation (magnesium chloride, calcium chloride), 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 1.74→88.36 Å / Num. obs: 68147 / % possible obs: 98.68 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.074 / Rrim(I) all: 0.19 / Net I/σ(I): 6.2
Reflection shellResolution: 1.74→1.81 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6108 / CC1/2: 0.336 / % possible all: 89.18

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosetta model

Resolution: 1.9→88.356 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.06 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2159 1567 2.94 %
Rwork0.1847 51644 -
obs0.1925 53261 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.77 Å2 / Biso mean: 31.5168 Å2 / Biso min: 15.34 Å2
Refinement stepCycle: final / Resolution: 1.9→88.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4299 0 0 257 4556
Biso mean---33.13 -
Num. residues----569
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9007-1.9620.36811500.33434705485597
1.962-2.03210.2881400.29594679481997
2.0321-2.11350.31311380.26874664480297
2.1135-2.20970.26381440.24674674481897
2.2097-2.32620.25821380.2194654479297
2.3262-2.47190.26171440.19254673481797
2.4719-2.66280.21261440.19274708485297
2.6628-2.93080.23181370.18164679481697
2.9308-3.35480.18821380.18274705484397
3.3548-4.22650.17161440.14714726487097
4.2265-57.96790.19861460.16224777492396
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)
10.00270.0008-0.00010.0006-0.00080.0015-0.00060.0212-0.0162-0.0068-0.0003-0.00340.0080.00390.00020.34260.001-0.02950.4974-0.02940.137738.44425.95637.028
20.0035-0.00020.0080.0392-0.00340.0217-0.0082-0.0182-0.0181-0.02470.01840.01320.0044-0.00960.00950.11960.0031-0.00630.3770.00420.084728.17529.79159.135
30.0001-0.0002-0.00060.00510.01160.0260.00350.01980.0030.01470.00050.006-0.0039-0.00940.00220.1166-0.0036-0.00240.3592-0.00960.084529.2739.54377.899
40.00840.00230.0050.00250.00050.0163-0.0017-0.010.0015-0.00480.00860.0037-0.0015-0.00710.00740.1298-0.01120.00020.40820.02080.100521.80336.42343.254
50.0087-0.0051-0.0130.01910.00710.01970.00450.00390.0088-0.0044-0.0046-0.0013-0.00420.0023-0.04050.1055-0.0020.00420.39280.02040.08733.237.95859.106
60.00130.0011-0.00310.0015-0.00330.0086-0.00650.01250.00250.00260.0087-0.0045-0.00320.009-0.00120.1045-0.0007-0.010.30550.02140.076544.13728.22776.921
70.00120.00280.00030.00740.0010.0002-0.00350.00180.0027-0.02790.0066-0.0026-0.00750.01740.00080.18020.0011-0.01270.38410.00840.093239.89243.61544.596
80.0111-0.0009-0.0040.02660.01050.0065-0.00590.01720.0025-0.02360.0154-0.0032-0.00810.00840.05320.1212-0.01580.0030.4168-0.00270.092537.49929.77657.664
90.0055-0.004-0.00090.00370.00070.00020.0029-0.00230.00220.0120.00880.01820.0058-0.01090.00190.2536-0.02260.04230.42340.03480.165124.74721.00278.86
100.0144-0.00310.00910.0019-0.00760.0329-0.005-0.0152-0.00330.01340.0061-0.00570.00650.0132-0.00450.2399-0.0062-0.02520.3755-0.030.098913.49649.85797.43
110.0140.0028-0.00110.02020.00530.0018-0.00090.00850.00510.00410.00490.0016-0.0013-0.01720.05160.10790.00820.00490.39260.00480.08253.30943.10269.876
120.0219-0.00630.00930.00610.00150.0191-0.00430.0152-0.00330.00390.01010.0065-0.0005-0.01230.00580.1304-0.00880.00380.33940.00360.0821-3.35439.97692.702
130.01790.00720.00880.0117-0.0010.0170.01090.00610.00310.0004-0.0201-0.0030.00210.0026-0.03710.0946-0.004-0.00250.36880.03060.08397.71738.51576.904
140.0001-0.0001-0.0001-0-0-00-0.00960.0019-0.00910.0055-0.0071-0.00480.0148-0.00840.13250.00270.01650.34940.04260.097419.16948.21759.088
150.01370.0025-0.00990.03270.02090.0233-0.0050.00190.00530.041-0.0183-0.00590.0144-0.0045-0.0220.18770.0085-0.0120.41210.00560.101414.34632.49891.516
160.01330.00660.00260.010.00450.002-0.0046-0.0328-0.00450.04270.011-0.00490.01180.00960.020.13960.0087-0.00140.3733-0.00920.083712.34346.49978.194
170.00230.000200000.00690.00660.0067-0.0061-0.0010.012-0.0049-0.0047-00.30470.03820.00240.43510.07560.2261-0.1555.37956.634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:23 )A5 - 23
2X-RAY DIFFRACTION2( CHAIN A AND RESID 24:69 )A24 - 69
3X-RAY DIFFRACTION3( CHAIN A AND RESID 70:93 )A70 - 93
4X-RAY DIFFRACTION4( CHAIN B AND RESID 0:23 )B0 - 23
5X-RAY DIFFRACTION5( CHAIN B AND RESID 24:68 )B24 - 68
6X-RAY DIFFRACTION6( CHAIN B AND RESID 69:93 )B69 - 93
7X-RAY DIFFRACTION7( CHAIN C AND RESID 0:23 )C0 - 23
8X-RAY DIFFRACTION8( CHAIN C AND RESID 24:68 )C24 - 68
9X-RAY DIFFRACTION9( CHAIN C AND RESID 69:90 )C69 - 90
10X-RAY DIFFRACTION10( CHAIN D AND RESID 3:23 )D3 - 23
11X-RAY DIFFRACTION11( CHAIN D AND RESID 24:93 )D24 - 93
12X-RAY DIFFRACTION12( CHAIN E AND RESID 0:23 )E0 - 23
13X-RAY DIFFRACTION13( CHAIN E AND RESID 24:68 )E24 - 68
14X-RAY DIFFRACTION14( CHAIN E AND RESID 69:93 )E69 - 93
15X-RAY DIFFRACTION15( CHAIN F AND RESID -1:23 )F-1 - 23
16X-RAY DIFFRACTION16( CHAIN F AND RESID 24:68 )F24 - 68
17X-RAY DIFFRACTION17( CHAIN F AND RESID 69:90 )F69 - 90

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