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- PDB-5e6g: Crystal Structure of De Novo Designed Protein CA01 -

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Basic information

Entry
Database: PDB / ID: 5e6g
TitleCrystal Structure of De Novo Designed Protein CA01
ComponentsDe novo designed protein CA01
KeywordsDE NOVO PROTEIN / Computational Design / Protein Engineering
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.09 Å
AuthorsJacobs, T.M. / Williams, T. / Kuhlman, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM073960 United States
CitationJournal: Science / Year: 2016
Title: Design of structurally distinct proteins using strategies inspired by evolution.
Authors: Jacobs, T.M. / Williams, B. / Williams, T. / Xu, X. / Eletsky, A. / Federizon, J.F. / Szyperski, T. / Kuhlman, B.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: De novo designed protein CA01
B: De novo designed protein CA01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4356
Polymers31,0612
Non-polymers3744
Water2,306128
1
A: De novo designed protein CA01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6252
Polymers15,5301
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo designed protein CA01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8104
Polymers15,5301
Non-polymers2793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: De novo designed protein CA01
B: De novo designed protein CA01
hetero molecules

A: De novo designed protein CA01
B: De novo designed protein CA01
hetero molecules

A: De novo designed protein CA01
B: De novo designed protein CA01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,30518
Polymers93,1836
Non-polymers1,12212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11900 Å2
ΔGint-85 kcal/mol
Surface area28430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.537, 116.537, 57.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-201-

PO4

21B-201-

PO4

31B-201-

PO4

41A-339-

HOH

51A-358-

HOH

61B-327-

HOH

71B-354-

HOH

DetailsMonomer according to SEC/MALS

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Components

#1: Protein De novo designed protein CA01


Mass: 15530.472 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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris:HCL, pH 8.5 - 1.0M Ammonium Phosphate Dibasic

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Data collection

DiffractionMean temperature: 63 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→58.27 Å / Num. obs: 17000 / % possible obs: 98.6 % / Redundancy: 3.1 % / Net I/σ(I): 13.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.09→37.85 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1596 5.11 %
Rwork0.2 --
obs0.202 31223 90.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 22 128 1980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031876
X-RAY DIFFRACTIONf_angle_d0.6162521
X-RAY DIFFRACTIONf_dihedral_angle_d14.964728
X-RAY DIFFRACTIONf_chiral_restr0.026265
X-RAY DIFFRACTIONf_plane_restr0.002334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.086-2.15330.3871480.33242201X-RAY DIFFRACTION75
2.1533-2.23030.34371400.31032701X-RAY DIFFRACTION92
2.2303-2.31960.31951550.30732689X-RAY DIFFRACTION90
2.3196-2.42510.26791390.23152772X-RAY DIFFRACTION92
2.4251-2.55290.28351500.21682741X-RAY DIFFRACTION93
2.5529-2.71280.23231560.19942776X-RAY DIFFRACTION93
2.7128-2.92220.21751420.1992776X-RAY DIFFRACTION93
2.9222-3.21620.26021320.19762795X-RAY DIFFRACTION93
3.2162-3.68120.2381380.17622770X-RAY DIFFRACTION92
3.6812-4.63660.16861430.15762691X-RAY DIFFRACTION90
4.6366-37.85170.19741530.1782715X-RAY DIFFRACTION91

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