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- PDB-9ntk: Chimeric Adenosine deaminase growth factor (ADGF) in complex with... -

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Basic information

Entry
Database: PDB / ID: 9ntk
TitleChimeric Adenosine deaminase growth factor (ADGF) in complex with pentostatin monophosphate
ComponentsAdenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
KeywordsHYDROLASE / Chimeric Adenosine deaminase growth factor (ADGF) apoenzyme / Adenosine deaminase / Pentostatin mono phosphate / Deoxycoformycin 5' phosphate
Function / homology
Function and homology information


2'-deoxyadenosine deaminase activity / inosine biosynthetic process / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / 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: 2.53 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: To Be Published
Title: Structural basis of substrate specificity of Helix pomatia AMP deaminase and a chimeric ADGF adenosine deaminase
Authors: Kaur, G. / Horton, J.R. / Cheng, X.
History
DepositionMar 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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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
C: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
D: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,07446
Polymers245,5334
Non-polymers8,54142
Water2,126118
1
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)127,09924
Polymers122,7662
Non-polymers4,33322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
D: Adenosine deaminase AGSA,Adenosine deaminase AGSA,Chimeric Adenosine deaminase growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,97522
Polymers122,7662
Non-polymers4,20920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.834, 118.477, 109.546
Angle α, β, γ (deg.)90.000, 98.488, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 28 - 521 / Label seq-ID: 28 - 521

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD

NCS oper:
IDCodeMatrixVector
1given(-0.999994670135, 0.00316939766919, -0.000783976894721), (0.00314250597446, 0.999476315316, 0.0322058966442), (0.000885639631787, 0.0322032613391, -0.999480948093)-35.4921386892, 0.0721610717602, -0.0859734303836
2given(-0.957267258066, -0.012767255718, -0.288922816365), (0.0111395285548, -0.999911470941, 0.00727744355926), (-0.288990151283, 0.00374799447867, 0.957324733306)-42.9118814073, -25.1870139195, 49.0710464228
3given(0.956617454718, -0.0129961973277, 0.291056943199), (-0.00278608654573, -0.999366984579, -0.0354664327912), (0.291333628424, 0.0331168988312, -0.956048109648)-8.74869676925, -25.4164472743, 59.3494275229

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4 / 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

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Sugars , 2 types, 16 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 12
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

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Non-polymers , 5 types, 144 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-A1CDW / pentostatin 5'-phosphate / (8S)-3-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol / 2'-deoxycoformycin 5'-phosphate


Mass: 348.249 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C11H17N4O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.53→29.63 Å / Num. obs: 76443 / % possible obs: 97.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 37.72 Å2 / CC1/2: 0.96 / Rpim(I) all: 0.163 / Net I/σ(I): 4.6
Reflection shellResolution: 2.53→2.59 Å / Redundancy: 2.5 % / Num. unique obs: 5236 / CC1/2: 0.372 / Rpim(I) all: 0.985

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→29.63 Å / SU ML: 0.4046 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 1998 2.62 %
Rwork0.2116 74358 -
obs0.2127 76356 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.35 Å2
Refinement stepCycle: LAST / Resolution: 2.53→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15960 0 544 118 16622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005716886
X-RAY DIFFRACTIONf_angle_d0.879522904
X-RAY DIFFRACTIONf_chiral_restr0.05122596
X-RAY DIFFRACTIONf_plane_restr0.00682896
X-RAY DIFFRACTIONf_dihedral_angle_d15.04176578
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.5420677995
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.604458811636
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.619541079966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.590.34011310.32254907X-RAY DIFFRACTION89.92
2.59-2.660.33961450.29815361X-RAY DIFFRACTION98.48
2.66-2.740.34711440.28025375X-RAY DIFFRACTION98.26
2.74-2.830.36241440.27825348X-RAY DIFFRACTION98.25
2.83-2.930.31671420.2715296X-RAY DIFFRACTION98.21
2.93-3.040.32231450.26845363X-RAY DIFFRACTION98.2
3.04-3.180.3181450.24485388X-RAY DIFFRACTION98.56
3.18-3.350.25821450.22265380X-RAY DIFFRACTION98.41
3.35-3.560.24771430.20925322X-RAY DIFFRACTION97.92
3.56-3.830.27971430.19265342X-RAY DIFFRACTION97.49
3.83-4.220.19721430.1695346X-RAY DIFFRACTION97.43
4.22-4.830.16851440.14735295X-RAY DIFFRACTION97
4.83-6.070.24561430.16985337X-RAY DIFFRACTION96.7
6.07-29.630.17131410.16585298X-RAY DIFFRACTION94.95

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