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- PDB-6czh: Structure of a redesigned beta barrel, mFAP0, bound to DFHBI -

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Basic information

Entry
Database: PDB / ID: 6czh
TitleStructure of a redesigned beta barrel, mFAP0, bound to DFHBI
ComponentsmFAP0
KeywordsDE NOVO PROTEIN / beta barrel / Rossetta / computational / de novo / ligand binder
Function / homologyChem-38E
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsDoyle, L.A. / Stoddard, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115545 United States
CitationJournal: Nature / Year: 2018
Title: De novo design of a fluorescence-activating beta-barrel.
Authors: Dou, J. / Vorobieva, A.A. / Sheffler, W. / Doyle, L.A. / Park, H. / Bick, M.J. / Mao, B. / Foight, G.W. / Lee, M.Y. / Gagnon, L.A. / Carter, L. / Sankaran, B. / Ovchinnikov, S. / Marcos, E. ...Authors: Dou, J. / Vorobieva, A.A. / Sheffler, W. / Doyle, L.A. / Park, H. / Bick, M.J. / Mao, B. / Foight, G.W. / Lee, M.Y. / Gagnon, L.A. / Carter, L. / Sankaran, B. / Ovchinnikov, S. / Marcos, E. / Huang, P.S. / Vaughan, J.C. / Stoddard, B.L. / Baker, D.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Structure summary
Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mFAP0
B: mFAP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9804
Polymers24,4752
Non-polymers5042
Water2,324129
1
A: mFAP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4902
Polymers12,2381
Non-polymers2521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mFAP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4902
Polymers12,2381
Non-polymers2521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.061, 59.382, 72.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mFAP0


Mass: 12237.574 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-38E / (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one


Mass: 252.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10F2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19723 / % possible obs: 98.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 16.71 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Rrim(I) all: 0.066 / Χ2: 0.911 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.839.20.4348440.9720.1430.4580.91986.9
1.83-1.869.50.419370.9720.1330.4320.88494.3
1.86-1.910.30.3559470.9770.1130.3740.93497.7
1.9-1.9410.40.3029780.9840.0960.3180.90899.2
1.94-1.9811.10.2479840.9890.0760.2590.96299.6
1.98-2.0311.60.219680.9940.0640.220.947100
2.03-2.0812.60.1989940.9930.0580.2060.963100
2.08-2.1313.10.1739760.9940.050.180.933100
2.13-2.2130.1469970.9930.0420.1520.923100
2.2-2.2712.70.1289500.9950.0370.1340.922100
2.27-2.35120.11110040.9950.0330.1160.915100
2.35-2.4412.40.0959850.9960.0280.0990.883100
2.44-2.5512.60.0819930.9960.0240.0850.849100
2.55-2.6912.80.06910020.9960.020.0720.84699.9
2.69-2.8612.70.069970.9980.0170.0630.849100
2.86-3.0811.80.0539900.9990.0160.0560.872100
3.08-3.3911.80.04810060.9970.0140.050.862100
3.39-3.8811.90.04910270.9980.0140.0510.885100
3.88-4.8810.80.04910340.9980.0150.0520.92999.2
4.88-5010.40.05211100.9980.0170.0551.05199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å48.06 Å
Translation1.8 Å48.06 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.024 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.56
RfactorNum. reflection% reflection
Rfree0.2415 1892 10 %
Rwork0.2054 --
obs0.209 18915 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.45 Å2 / Biso mean: 22.1413 Å2 / Biso min: 3.91 Å2
Refinement stepCycle: final / Resolution: 1.8→46.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 56 129 1763
Biso mean--14.4 32.74 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031703
X-RAY DIFFRACTIONf_angle_d0.6942350
X-RAY DIFFRACTIONf_chiral_restr0.045282
X-RAY DIFFRACTIONf_plane_restr0.004297
X-RAY DIFFRACTIONf_dihedral_angle_d9.4091011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7999-1.8450.3067950.245985294767
1.845-1.89480.28171100.2284995110579
1.8948-1.95060.27541210.23041091121287
1.9506-2.01360.24431330.22651196132994
2.0136-2.08550.26851390.22531245138499
2.0855-2.1690.25291410.223512711412100
2.169-2.26770.2691400.212312531393100
2.2677-2.38730.2771420.2212861428100
2.3873-2.53690.26081430.210912811424100
2.5369-2.73270.2461420.21312771419100
2.7327-3.00770.25791420.216412891431100
3.0077-3.44280.23551440.205312961440100
3.4428-4.3370.21171460.171413101456100
4.337-46.03950.20061540.19041381153599

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