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- PDB-7vus: Crystal structure of AlleyCat9 with 5-nitro-benzotriazole -

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Basic information

Entry
Database: PDB / ID: 7vus
TitleCrystal structure of AlleyCat9 with 5-nitro-benzotriazole
ComponentsAlleyCat
KeywordsBIOSYNTHETIC PROTEIN/INHIBITOR / artificial / enzyme / calmodulin / BIOSYNTHETIC PROTEIN-INHIBITOR COMPLEX
Function / homology5-nitro-1H-benzotriazole
Function and homology information
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: AlleyCat
B: AlleyCat
C: AlleyCat
D: AlleyCat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,51525
Polymers34,0214
Non-polymers1,49421
Water2,432135
1
A: AlleyCat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7494
Polymers8,5051
Non-polymers2443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-30 kcal/mol
Surface area4170 Å2
MethodPISA
2
B: AlleyCat
D: AlleyCat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,97616
Polymers17,0102
Non-polymers96514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-114 kcal/mol
Surface area7690 Å2
MethodPISA
3
C: AlleyCat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7905
Polymers8,5051
Non-polymers2844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-40 kcal/mol
Surface area4050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.971, 82.971, 104.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11D-404-

HOH

21D-441-

HOH

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Components

#1: Protein
AlleyCat


Mass: 8505.151 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-3NY / 5-nitro-1H-benzotriazole


Mass: 164.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, HEPES, calcium chloride, sodium chloride, 5-nitro-benzotriazole

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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→12.98 Å / Num. obs: 40502 / % possible obs: 99.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 14.59 Å2 / CC1/2: 0.998 / R split: 0.06 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.045 / Net I/σ(I): 15.8
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2100 / Rpim(I) all: 0.615

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→12.98 Å / SU ML: 0.1923 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2522 1947 4.83 %
Rwork0.2137 38341 -
obs0.2156 40288 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→12.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 79 135 2313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882185
X-RAY DIFFRACTIONf_angle_d1.01092940
X-RAY DIFFRACTIONf_chiral_restr0.056303
X-RAY DIFFRACTIONf_plane_restr0.0093408
X-RAY DIFFRACTIONf_dihedral_angle_d15.3977833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.28481390.26182664X-RAY DIFFRACTION99.26
1.74-1.790.32361340.26392697X-RAY DIFFRACTION99.93
1.79-1.840.28931400.25412712X-RAY DIFFRACTION99.96
1.84-1.90.3131370.25352723X-RAY DIFFRACTION99.97
1.9-1.970.34031310.24512706X-RAY DIFFRACTION99.96
1.97-2.050.25921250.23342735X-RAY DIFFRACTION99.97
2.05-2.140.24761370.22392710X-RAY DIFFRACTION99.41
2.14-2.250.24981190.20732737X-RAY DIFFRACTION99.41
2.25-2.390.23181480.21632711X-RAY DIFFRACTION99.41
2.39-2.580.23921360.20992737X-RAY DIFFRACTION99.1
2.58-2.830.27821460.20912733X-RAY DIFFRACTION99.38
2.83-3.240.24371610.20512739X-RAY DIFFRACTION99.28
3.24-4.060.21881410.18492799X-RAY DIFFRACTION99.19
4.06-12.980.23071530.19822938X-RAY DIFFRACTION99.26

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