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- PDB-6mct: A designed pentameric membrane protein stabilized by van der Waal... -

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Basic information

Entry
Database: PDB / ID: 6mct
TitleA designed pentameric membrane protein stabilized by van der Waals interaction
Componentsmini-eVgL membrane protein
KeywordsDE NOVO PROTEIN / Membrane protein / protein design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMravic, M. / Liu, L. / Degrado, W.F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122603 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117593 United States
National Science Foundation (NSF, United States)CHE1413295 United States
CitationJournal: Science / Year: 2019
Title: Packing of apolar side chains enables accurate design of highly stable membrane proteins.
Authors: Mravic, M. / Thomaston, J.L. / Tucker, M. / Solomon, P.E. / Liu, L. / DeGrado, W.F.
History
DepositionSep 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / pdbx_entity_src_syn
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 3, 2024Group: 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: mini-eVgL membrane protein
B: mini-eVgL membrane protein
C: mini-eVgL membrane protein
D: mini-eVgL membrane protein
E: mini-eVgL membrane protein
F: mini-eVgL membrane protein
G: mini-eVgL membrane protein
H: mini-eVgL membrane protein
I: mini-eVgL membrane protein
J: mini-eVgL membrane protein
K: mini-eVgL membrane protein
L: mini-eVgL membrane protein
M: mini-eVgL membrane protein
N: mini-eVgL membrane protein
O: mini-eVgL membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,10539
Polymers45,43315
Non-polymers5,67224
Water99155
1
A: mini-eVgL membrane protein
B: mini-eVgL membrane protein
C: mini-eVgL membrane protein
D: mini-eVgL membrane protein
E: mini-eVgL membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,36715
Polymers15,1445
Non-polymers2,22310
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-138 kcal/mol
Surface area10250 Å2
MethodPISA
2
F: mini-eVgL membrane protein
G: mini-eVgL membrane protein
H: mini-eVgL membrane protein
I: mini-eVgL membrane protein
J: mini-eVgL membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,86912
Polymers15,1445
Non-polymers1,7247
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-85 kcal/mol
Surface area9200 Å2
MethodPISA
3
K: mini-eVgL membrane protein
L: mini-eVgL membrane protein
M: mini-eVgL membrane protein
N: mini-eVgL membrane protein
O: mini-eVgL membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,86912
Polymers15,1445
Non-polymers1,7247
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-91 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.894, 165.630, 41.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide
mini-eVgL membrane protein


Mass: 3028.867 Da / Num. of mol.: 15 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.98 Å3/Da / Density % sol: 37.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 5 mg/ml protein in 45 mM C8E4 mixed (1:1) with 2.5M ammonium sulfate, 50 mM Hepes pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.89→55 Å / Num. obs: 29360 / % possible obs: 99.6 % / Redundancy: 12.6 % / Biso Wilson estimate: 28.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.113 / Net I/σ(I): 14.49
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.384 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 2896 / CC1/2: 0.718 / Rrim(I) all: 1.44 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: designed

Resolution: 1.9→50.387 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.12
RfactorNum. reflection% reflection
Rfree0.2135 1432 4.89 %
Rwork0.1788 --
obs0.1805 29275 99.65 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 1.9→50.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 301 55 3596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163635
X-RAY DIFFRACTIONf_angle_d1.2294842
X-RAY DIFFRACTIONf_dihedral_angle_d24.1411361
X-RAY DIFFRACTIONf_chiral_restr0.227623
X-RAY DIFFRACTIONf_plane_restr0.014487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.9680.28251600.24362734X-RAY DIFFRACTION100
1.968-2.04680.28141460.21792742X-RAY DIFFRACTION100
2.0468-2.13990.25881150.19522733X-RAY DIFFRACTION100
2.1399-2.25270.22931420.18852744X-RAY DIFFRACTION100
2.2527-2.39390.1921400.16812786X-RAY DIFFRACTION100
2.3939-2.57870.1941430.15382764X-RAY DIFFRACTION100
2.5787-2.83820.21151440.15892747X-RAY DIFFRACTION100
2.8382-3.24880.22581340.16442813X-RAY DIFFRACTION100
3.2488-4.09290.18371430.16172857X-RAY DIFFRACTION100
4.0929-50.40470.21251650.19372923X-RAY DIFFRACTION98
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)
13.2610.98841.28626.1187-1.15727.8304-0.0335-0.1335-0.1388-0.15610.06190.21311.35580.00280.00750.1378-0.0057-0.01270.1304-0.00120.3468-13.541329.0486-3.0986
23.0509-1.7188-2.77213.55121.25532.81120.02760.0543-0.1254-0.0557-0.05390.21690.0021-0.47080.07970.11330.0006-0.00990.1910.01770.3261-18.599237.9374-2.3999
32.7453-0.1754-1.82922.96681.3283.0719-0.0677-0.06520.1262-0.1206-0.08350.116-0.7615-0.47080.28180.14670.007-0.00080.09780.01170.3186-11.729945.189-2.7296
44.39840.11253.06111.13471.23948.6173-0.07850.03610.116-0.02620.02360.0768-0.50560.52020.09970.1358-0.02050.02710.1627-0.01560.3345-2.792141.0236-2.9693
56.0114-0.6541.11133.34860.29866.88830.08390.0979-0.1122-0.1075-0.2678-0.11570.68090.82750.21610.1460.0347-0.02180.1355-0.00630.3157-3.72130.9766-3.1667
64.55060.36232.26895.9832-0.94088.3668-0.2785-0.04620.20820.09870.05760.0525-0.5959-0.31070.24120.18870.06490.01910.1747-0.03930.3404-13.595172.62493.2841
77.15280.3137-0.16924.2525-2.41454.7531-0.1237-0.3417-0.1645-0.2960.04690.3118-0.2497-0.98230.10240.14010.0367-0.02050.20590.00410.3816-18.615363.84833.1046
85.9919-0.9745-0.46923.148-1.1352.9274-0.4021-0.2155-0.319-0.096-0.21810.0670.7618-0.10720.60210.2013-0.0180.01730.1255-0.01060.3234-11.713556.48232.7746
95.4492-1.1762-1.35823.10372.55467.8138-0.2737-0.2719-0.041-0.1210.15120.11790.84590.64310.12550.18010.02230.03020.1477-0.030.3758-2.291160.88712.6896
105.05831.2577-1.46516.7804-1.46318.1341-0.0993-0.04240.2829-0.1029-0.2928-0.2193-0.14530.4640.33520.14310.0233-0.00220.1505-0.03180.3937-3.737870.59333.2982
112.92521.5843-1.88188.14850.13562.5445-0.4988-0.04610.35130.6281-0.3275-0.129-1.49740.53190.60780.28280.0252-0.03730.0975-0.05270.3624-9.212817.7766-0.2057
125.5762-2.5592-1.03694.0979-2.59445.6076-0.3756-0.4154-0.33140.1868-0.04740.2138-1.072-1.25550.46180.18620.08040.03190.2527-0.02610.2939-17.86912.8966-0.2137
135.34951.26131.51717.2113-1.45015.75380.1423-0.3844-0.34760.2288-0.31750.18590.8162-1.5890.08920.1753-0.1078-0.02240.25920.06970.3254-16.07633.1226-0.3856
145.1223-1.7428-0.44357.51461.47479.238-0.248-0.2432-0.15580.255-0.0830.2171.42660.32510.31050.18470.0333-0.0290.1197-0.03440.3133-5.95511.9067-0.3376
156.91520.23592.20973.65930.83358.4083-0.03470.06410.25460.241-0.0099-0.3190.22860.55130.1030.1494-0.0061-0.03990.1073-0.02540.3625-1.778711.0736-0.1999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L
13X-RAY DIFFRACTION13chain M
14X-RAY DIFFRACTION14chain N
15X-RAY DIFFRACTION15chain O

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