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- PDB-9nti: Chimeric Adenosine deaminase growth factor (ADGF) apoenzyme -

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Basic information

Entry
Database: PDB / ID: 9nti
TitleChimeric Adenosine deaminase growth factor (ADGF) apoenzyme
ComponentsAdenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric adenosine deaminase growth factor
KeywordsHYDROLASE / Chimeric Adenosine deaminase growth factor (ADGF) apoenzyme / Adenosine deaminase
Function / homology
Function and homology information


inosine biosynthetic process / adenosine deaminase / adenosine deaminase activity / adenosine catabolic process / extracellular space / metal ion binding
Similarity search - Function
Adenosine deaminase-related growth factor / Adenosine/AMP deaminase N-terminal / Adenosine/AMP deaminase N-terminal / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolase
Similarity search - Domain/homology
Adenosine deaminase AGSA
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKaur, G. / Horton, J.R. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134744 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural basis for the substrate specificity of Helix pomatia AMP deaminase and a chimeric ADGF adenosine deaminase.
Authors: Kaur, G. / Horton, J.R. / Tzertzinis, G. / Zhou, J. / Schildkraut, I. / Cheng, X.
History
DepositionMar 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric adenosine deaminase growth factor
B: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric adenosine deaminase growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,22410
Polymers122,7662
Non-polymers1,4588
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-81 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.444, 109.268, 173.275
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 Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric adenosine deaminase growth factor / Atrial gland-specific antigen / AGSA / Mollusk-derived growth factor / MDGF


Mass: 61383.203 Da / Num. of mol.: 2 / Fragment: residues 1-120,residues 254-525
Source method: isolated from a genetically manipulated source
Details: residues 1-120 of A. californica AGSA, followed by active site region of H. pomatia Adenosine deaminase growth factor, followed by residues 254-525 of A. californica AGSA,residues 1-120 of A. ...Details: residues 1-120 of A. californica AGSA, followed by active site region of H. pomatia Adenosine deaminase growth factor, followed by residues 254-525 of A. californica AGSA,residues 1-120 of A. californica AGSA, followed by active site region of H. pomatia Adenosine deaminase growth factor, followed by residues 254-525 of A. californica AGSA,residues 1-120 of A. californica AGSA, followed by active site region of H. pomatia Adenosine deaminase growth factor, followed by residues 254-525 of A. californica AGSA
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Komagataella pastoris (fungus) / References: UniProt: P15287, adenosine deaminase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate trihydrate pH 4.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→46.21 Å / Num. obs: 519122 / % possible obs: 99.33 % / Redundancy: 19.2 % / CC1/2: 0.985 / Rpim(I) all: 0.121 / Net I/σ(I): 7
Reflection shellResolution: 2.99→3.1 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2644 / CC1/2: 0.513 / Rpim(I) all: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→46.21 Å / SU ML: 0.5525 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.4145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2735 3737 7.41 %
Rwork0.216 46694 -
obs0.2202 50431 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7943 0 92 3 8038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00258231
X-RAY DIFFRACTIONf_angle_d0.676511182
X-RAY DIFFRACTIONf_chiral_restr0.0891247
X-RAY DIFFRACTIONf_plane_restr0.00411432
X-RAY DIFFRACTIONf_dihedral_angle_d13.09273116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.040.55461150.45271471X-RAY DIFFRACTION84.63
3.04-3.080.41471400.42571709X-RAY DIFFRACTION97.62
3.08-3.120.49951330.39981705X-RAY DIFFRACTION98.08
3.12-3.170.41181440.39231748X-RAY DIFFRACTION98.7
3.17-3.210.38531370.34251731X-RAY DIFFRACTION98.89
3.21-3.260.37861400.31551699X-RAY DIFFRACTION99.51
3.26-3.320.3841460.30581807X-RAY DIFFRACTION99.95
3.32-3.370.35731320.30571654X-RAY DIFFRACTION99.72
3.37-3.440.37381430.30091779X-RAY DIFFRACTION99.53
3.44-3.50.32021350.29291754X-RAY DIFFRACTION100
3.5-3.570.31941350.26721713X-RAY DIFFRACTION99.52
3.57-3.650.34171430.26451772X-RAY DIFFRACTION99.84
3.65-3.740.23671400.24071740X-RAY DIFFRACTION99.95
3.74-3.830.30361440.21921750X-RAY DIFFRACTION99.89
3.83-3.930.27641440.20851749X-RAY DIFFRACTION99.58
3.93-4.050.26181410.19651743X-RAY DIFFRACTION99.95
4.05-4.180.27541350.19041728X-RAY DIFFRACTION99.89
4.18-4.330.28891450.17561778X-RAY DIFFRACTION100
4.33-4.50.23371380.17051712X-RAY DIFFRACTION99.95
4.5-4.710.20391350.16691739X-RAY DIFFRACTION99.89
4.71-4.950.21711380.15951777X-RAY DIFFRACTION99.9
4.95-5.260.22051350.17421727X-RAY DIFFRACTION100
5.26-5.670.31751420.18861742X-RAY DIFFRACTION99.95
5.67-6.240.27261330.19511741X-RAY DIFFRACTION99.84
6.24-7.140.24851460.19431752X-RAY DIFFRACTION99.95
7.14-8.980.22191330.17431745X-RAY DIFFRACTION100
8.98-46.210.18171450.16681729X-RAY DIFFRACTION99

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