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- PDB-6msq: Crystal structure of pRO-2.3 -

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Basic information

Entry
Database: PDB / ID: 6msq
TitleCrystal structure of pRO-2.3
ComponentspRO-2.3
KeywordsDE NOVO PROTEIN / Computational Design / helical bundle
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsBoyken, S.E. / Sankaran, B. / Bick, M.J. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2019
Title: De novo design of tunable, pH-driven conformational changes.
Authors: Boyken, S.E. / Benhaim, M.A. / Busch, F. / Jia, M. / Bick, M.J. / Choi, H. / Klima, J.C. / Chen, Z. / Walkey, C. / Mileant, A. / Sahasrabuddhe, A. / Wei, K.Y. / Hodge, E.A. / Byron, S. / ...Authors: Boyken, S.E. / Benhaim, M.A. / Busch, F. / Jia, M. / Bick, M.J. / Choi, H. / Klima, J.C. / Chen, Z. / Walkey, C. / Mileant, A. / Sahasrabuddhe, A. / Wei, K.Y. / Hodge, E.A. / Byron, S. / Quijano-Rubio, A. / Sankaran, B. / King, N.P. / Lippincott-Schwartz, J. / Wysocki, V.H. / Lee, K.K. / Baker, D.
History
DepositionOct 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _struct.title
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 18, 2020Group: Structure summary / Category: audit_author
Revision 1.4Mar 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pRO-2.3
B: pRO-2.3


Theoretical massNumber of molelcules
Total (without water)16,9782
Polymers16,9782
Non-polymers00
Water4,522251
1
A: pRO-2.3

A: pRO-2.3

A: pRO-2.3


Theoretical massNumber of molelcules
Total (without water)25,4663
Polymers25,4663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5990 Å2
ΔGint-42 kcal/mol
Surface area11460 Å2
MethodPISA
2
B: pRO-2.3

B: pRO-2.3

B: pRO-2.3


Theoretical massNumber of molelcules
Total (without water)25,4663
Polymers25,4663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6180 Å2
ΔGint-50 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.566, 50.566, 130.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-156-

HOH

21B-156-

HOH

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Components

#1: Protein pRO-2.3


Mass: 8488.750 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.: 251 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2M di-sodium tartrate and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999913 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2018
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999913 Å / Relative weight: 1
ReflectionResolution: 1.28→43.79 Å / Num. obs: 48515 / % possible obs: 99.8 % / Redundancy: 8.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.042 / Rrim(I) all: 0.125 / Net I/σ(I): 7.8
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 6.4 % / Rmerge(I) obs: 3.554 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2430 / CC1/2: 0.428 / Rpim(I) all: 1.536 / Rrim(I) all: 3.88 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_3112: ???)refinement
XDSJun 17, 2015data reduction
XDSJun 17, 2015data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational Design Model

Resolution: 1.28→43.79 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.24
RfactorNum. reflection% reflection
Rfree0.1944 1657 4.08 %
Rwork0.1726 --
obs0.1736 40645 83.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.28→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 0 251 1396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071182
X-RAY DIFFRACTIONf_angle_d0.7311605
X-RAY DIFFRACTIONf_dihedral_angle_d18.755446
X-RAY DIFFRACTIONf_chiral_restr0.044202
X-RAY DIFFRACTIONf_plane_restr0.005209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.31770.5024900.49982183X-RAY DIFFRACTION56
1.3177-1.36020.4191980.392412X-RAY DIFFRACTION62
1.3602-1.40880.45921260.40082797X-RAY DIFFRACTION72
1.4088-1.46520.31141190.30312710X-RAY DIFFRACTION71
1.4652-1.53190.34631250.25053018X-RAY DIFFRACTION77
1.5319-1.61270.21141420.16373430X-RAY DIFFRACTION88
1.6127-1.71370.18181380.15453599X-RAY DIFFRACTION93
1.7137-1.84610.1931590.16453653X-RAY DIFFRACTION94
1.8461-2.03180.19781660.17393668X-RAY DIFFRACTION94
2.0318-2.32580.18451650.15343795X-RAY DIFFRACTION98
2.3258-2.93020.16171720.1523886X-RAY DIFFRACTION100
2.9302-43.81730.16761570.15533837X-RAY DIFFRACTION97

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