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- PDB-7vur: Crystal structure of AlleyCat9 with calcium but no inhibitor -

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Basic information

Entry
Database: PDB / ID: 7vur
TitleCrystal structure of AlleyCat9 with calcium but no inhibitor
ComponentsAlleyCat
KeywordsBIOSYNTHETIC PROTEIN / Artificial / enzyme / calmodulin
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMargheritis, E. / Takahashi, K. / Korendovych, I.V. / Tame, J.R.H.
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 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AlleyCat
B: AlleyCat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4479
Polymers17,0102
Non-polymers4377
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-86 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.376, 58.711, 87.510
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 AlleyCat


Mass: 8505.151 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MPD, HEPES pH 7, 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→12.75 Å / Num. obs: 16079 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 10.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Net I/σ(I): 13.6
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 806 / Rpim(I) all: 0.177 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1iwq

1iwq


Resolution: 1.7→12.75 Å / SU ML: 0.1523 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 18.1485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2144 819 5.11 %
Rwork0.1786 15216 -
obs0.1804 16035 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.62 Å2
Refinement stepCycle: LAST / Resolution: 1.7→12.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 21 92 1181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551092
X-RAY DIFFRACTIONf_angle_d0.81851469
X-RAY DIFFRACTIONf_chiral_restr0.0504155
X-RAY DIFFRACTIONf_plane_restr0.0051204
X-RAY DIFFRACTIONf_dihedral_angle_d15.1106425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.810.24981360.18922455X-RAY DIFFRACTION98.44
1.81-1.950.21481410.17192489X-RAY DIFFRACTION99.28
1.95-2.140.21971360.16292487X-RAY DIFFRACTION99.43
2.14-2.450.21731360.16722524X-RAY DIFFRACTION99.48
2.45-3.080.21231410.18692564X-RAY DIFFRACTION99.67
3.08-12.750.2011290.1862697X-RAY DIFFRACTION99.72

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