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- PDB-6z0c: Structure of in silico modelled artificial Maquette-3 protein -

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Basic information

Entry
Database: PDB / ID: 6z0c
TitleStructure of in silico modelled artificial Maquette-3 protein
ComponentsMaquette-3
KeywordsDE NOVO PROTEIN / four-helix bundle / hydrophobic core / ion-pair stabilization / structural stability / extremophile
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBaumgart, M. / Roepke, M. / Muehlbauer, M.E. / Asami, S. / Mader, S.L. / Fredriksson, K. / Groll, M. / Gamiz-Hernandez, A.P. / Kaila, V.R.I.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035 Germany
European Research Council (ERC)no. 715311European Union
CitationJournal: Nat Commun / Year: 2021
Title: Design of buried charged networks in artificial proteins
Authors: Baumgart, M. / Ropke, M. / Muhlbauer, M.E. / Asami, S. / Mader, S.L. / Fredriksson, K. / Groll, M. / Gamiz-Hernandez, A.P. / Kaila, V.R.I.
History
DepositionMay 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 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: Maquette-3
B: Maquette-3
C: Maquette-3
D: Maquette-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1866
Polymers94,1084
Non-polymers782
Water2,216123
1
A: Maquette-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5662
Polymers23,5271
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maquette-3


Theoretical massNumber of molelcules
Total (without water)23,5271
Polymers23,5271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Maquette-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5662
Polymers23,5271
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Maquette-3


Theoretical massNumber of molelcules
Total (without water)23,5271
Polymers23,5271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.690, 65.900, 68.260
Angle α, β, γ (deg.)89.860, 90.290, 117.360
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Maquette-3


Mass: 23527.049 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, 1.5 M Potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 80776 / % possible obs: 97.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.3
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 11918 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in silico Maquette model

Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.939 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 4038 5 %RANDOM
Rwork0.1893 ---
obs0.1886 76730 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.27 Å2 / Biso mean: 41.218 Å2 / Biso min: 28.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20.7 Å20.93 Å2
2---1.18 Å20.12 Å2
3----0.76 Å2
Refinement stepCycle: final / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 2 123 6613
Biso mean--41.15 46.2 -
Num. residues----783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136534
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176412
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.6378736
X-RAY DIFFRACTIONr_angle_other_deg1.1651.57315059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4175777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8626.298389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.897151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1071528
X-RAY DIFFRACTIONr_chiral_restr0.0540.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021071
X-RAY DIFFRACTIONr_rigid_bond_restr0.776312946
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 302 -
Rwork0.278 5743 -
all-6045 -
obs--98.63 %
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)
10.0386-0.0961-0.06670.24650.17290.1223-0.0024-0.001-0.0016-0.00290.00770.0026-0.00260.0084-0.00540.0062-0.0053-0.01070.0071-0.00180.06755.7532.634815.3348
20.0714-0.04550.01170.37990.06230.0159-0.0023-0.0004-0.00810.0140.0062-0.00010.00210.0015-0.0040.006-0.0053-0.01180.00870.00120.0652-10.912220.36364.9337
30.0418-0.10050.07370.2696-0.19840.1463-0.0001-0.00090.0011-0.00250.00320.0010.0031-0.0039-0.00310.0053-0.0048-0.01330.00760.00180.0669-36.113725.8134-18.6803
40.0634-0.04090.00050.4216-0.06510.0107-0.0014-0.00090.00810.01220.0036-0.0061-0.0013-0.0006-0.00220.0054-0.0049-0.01240.0094-0.00020.064-19.37238.248-29.2195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 200
2X-RAY DIFFRACTION2B2 - 197
3X-RAY DIFFRACTION3C2 - 199
4X-RAY DIFFRACTION4D2 - 197

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