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- PDB-7vuu: Crystal structure of AlleyCat10 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 7vuu
TitleCrystal structure of AlleyCat10 with inhibitor
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: 1.95 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)35,58325
Polymers34,2454
Non-polymers1,33821
Water1,47782
1
A: AlleyCat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8866
Polymers8,5611
Non-polymers3245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-41 kcal/mol
Surface area4160 Å2
MethodPISA
2
B: AlleyCat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9267
Polymers8,5611
Non-polymers3656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-43 kcal/mol
Surface area4450 Å2
MethodPISA
3
D: AlleyCat
hetero molecules

C: AlleyCat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,77112
Polymers17,1222
Non-polymers64910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545-x+1/2,y-1/2,-z+3/41
Buried area1470 Å2
ΔGint-101 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.919, 82.919, 104.948
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-205-

HOH

21D-228-

HOH

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Components

#1: Protein
AlleyCat


Mass: 8561.241 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.: 17 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 53.3 %
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: 1.95→13.19 Å / Num. obs: 27277 / % possible obs: 99.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2844 / Rpim(I) all: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→13.19 Å / SU ML: 0.2514 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2784 1351 5.03 %
Rwork0.2485 25499 -
obs0.2501 26850 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.78 Å2
Refinement stepCycle: LAST / Resolution: 1.95→13.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 65 82 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612186
X-RAY DIFFRACTIONf_angle_d0.7632935
X-RAY DIFFRACTIONf_chiral_restr0.0449297
X-RAY DIFFRACTIONf_plane_restr0.0041412
X-RAY DIFFRACTIONf_dihedral_angle_d16.4027843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.38731240.30622529X-RAY DIFFRACTION98.22
2.02-2.10.36361230.31052398X-RAY DIFFRACTION95.2
2.1-2.20.30531210.26962516X-RAY DIFFRACTION98.32
2.2-2.310.29611500.24352537X-RAY DIFFRACTION99.81
2.31-2.450.30331370.24932532X-RAY DIFFRACTION99.26
2.45-2.640.29321280.27132519X-RAY DIFFRACTION98.29
2.64-2.910.25081460.26222559X-RAY DIFFRACTION99.45
2.91-3.320.29211460.2372566X-RAY DIFFRACTION98.98
3.32-4.160.22111380.21062595X-RAY DIFFRACTION98.74
4.16-13.190.24861380.23062748X-RAY DIFFRACTION99.35

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