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- PDB-7p9t: Crystal structure of CD73 in complex with dCMP in the open form -

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Basic information

Entry
Database: PDB / ID: 7p9t
TitleCrystal structure of CD73 in complex with dCMP in the open form
Components5'-nucleotidase
KeywordsHYDROLASE / ecto-5'-nucleotidase / eN / substrate
Function / homology
Function and homology information


thymidylate 5'-phosphatase / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process / : / IMP-specific 5'-nucleotidase / : / Nicotinate metabolism / Purine catabolism / : / 5'-nucleotidase / 5'-nucleotidase activity / leukocyte cell-cell adhesion / DNA metabolic process / response to ATP / ATP metabolic process / Purinergic signaling in leishmaniasis infection / calcium ion homeostasis / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
5'-nucleotidase signature 1. / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases ...5'-nucleotidase signature 1. / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.79 Å
AuthorsScaletti, E.R. / Strater, N.
CitationJournal: Purinergic Signal / Year: 2021
Title: Substrate binding modes of purine and pyrimidine nucleotides to human ecto-5'-nucleotidase (CD73) and inhibition by their bisphosphonic acid derivatives.
Authors: Scaletti, E. / Huschmann, F.U. / Mueller, U. / Weiss, M.S. / Strater, N.
History
DepositionJul 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9425
Polymers60,4641
Non-polymers4784
Water4,071226
1
A: 5'-nucleotidase
hetero molecules

A: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,88510
Polymers120,9292
Non-polymers9568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4430 Å2
ΔGint-194 kcal/mol
Surface area39630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.104, 132.846, 67.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 5'-nucleotidase / 5'-NT / Ecto-5'-nucleotidase


Mass: 60464.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Production host: Escherichia coli (E. coli) / References: UniProt: P21589, 5'-nucleotidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 7 mg/mL protein concentration, 100 mM Tris pH 7.8, 10 % PEG6000, equal amounts of protein and reservoir. Following crystal formation (1-2 days), the crystals were transferred to soaking ...Details: 7 mg/mL protein concentration, 100 mM Tris pH 7.8, 10 % PEG6000, equal amounts of protein and reservoir. Following crystal formation (1-2 days), the crystals were transferred to soaking solution containing reservoir solution and 50 mM dCMP. Crystals were then transferred to cryo solution containing an additional 20 % glycerol, soaked for ~2-5 min, and flash frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.8943 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 1.79→47.95 Å / Num. obs: 58377 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.059 / Rrim(I) all: 0.122 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.79-1.824.10.99432880.5460.5511.1499.1
9.12-47.913.40.0254890.9990.0150.02994.6

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4h2g

4h2g


Resolution: 1.79→47.95 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.14 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 2944 5.1 %RANDOM
Rwork0.1853 ---
obs0.1868 55272 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.68 Å2 / Biso mean: 19.897 Å2 / Biso min: 9.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0 Å2
2---0.32 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.79→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 23 226 4296
Biso mean--26.7 23.86 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0124311
X-RAY DIFFRACTIONr_angle_refined_deg1.91.6275899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0085571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42823.333207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58215723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.691520
X-RAY DIFFRACTIONr_chiral_restr0.1250.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023304
LS refinement shellResolution: 1.79→1.836 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 212 -
Rwork0.273 4054 -
all-4266 -
obs--99.77 %
Refinement TLS params.Method: refined / Origin x: 25.11 Å / Origin y: 24.935 Å / Origin z: 23.366 Å
111213212223313233
T0.0105 Å2-0.0054 Å2-0.0028 Å2-0.0155 Å2-0.0021 Å2--0.0028 Å2
L0.1285 °2-0.1025 °20.1149 °2-0.4174 °2-0.2278 °2--0.2136 °2
S-0.0084 Å °-0.0018 Å °0.0065 Å °-0.0438 Å °0.0084 Å °0.0091 Å °0.0025 Å °0.0234 Å °-0 Å °

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