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- PDB-7vut: Crystal structure of AlleyCat10 -

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Basic information

Entry
Database: PDB / ID: 7vut
TitleCrystal structure of AlleyCat10
ComponentsAlleyCat10
KeywordsBIOSYNTHETIC PROTEIN / Artificial / enzyme / calmodulin
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTame, J.R.H. / Korendovych, I.V. / Margheritis, E. / Takahashi, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119634 United States
CitationJournal: Nature / Year: 2022
Title: NMR-guided directed evolution.
Authors: Bhattacharya, S. / Margheritis, E.G. / Takahashi, K. / Kulesha, A. / D'Souza, A. / Kim, I. / Yoon, J.H. / Tame, J.R.H. / Volkov, A.N. / Makhlynets, O.V. / Korendovych, I.V.
History
DepositionNov 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AlleyCat10
B: AlleyCat10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3638
Polymers17,1222
Non-polymers2406
Water2,360131
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-63 kcal/mol
Surface area8140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.313, 50.499, 88.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein AlleyCat10


Mass: 8561.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.78 Å3/Da / Density % sol: 30.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MPD, HEPES, calcium chloride, sodium chloride

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.7→12.5 Å / Num. obs: 13978 / % possible obs: 99.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 8.59 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.058 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 701 / Rpim(I) all: 0.162

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→12.5 Å / SU ML: 0.1867 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.1271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 663 4.76 %
Rwork0.1972 13275 -
obs0.1996 13938 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 6 131 1221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551094
X-RAY DIFFRACTIONf_angle_d0.74051468
X-RAY DIFFRACTIONf_chiral_restr0.0486152
X-RAY DIFFRACTIONf_plane_restr0.0055208
X-RAY DIFFRACTIONf_dihedral_angle_d14.1232432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.26861210.22022558X-RAY DIFFRACTION97.92
1.83-2.010.26091430.20062601X-RAY DIFFRACTION99.67
2.01-2.30.24781280.1922654X-RAY DIFFRACTION99.96
2.3-2.90.25431300.19732660X-RAY DIFFRACTION99.96
2.9-12.50.22331410.19172802X-RAY DIFFRACTION99.8

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