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- PDB-6vca: TB38 complex -

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Basic information

Entry
Database: PDB / ID: 6vca
TitleTB38 complex
Components
  • 5'-nucleotidase, ecto (CD73), isoform CRA_a
  • TB38 heavy chain
  • TB38 light chain
KeywordsIMMUNE SYSTEM / Fab / Enzyme
Function / homology
Function and homology information


thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process / GMP 5'-nucleotidase activity / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / nucleotide catabolic process / Nicotinate metabolism / Purine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / DNA metabolic process / leukocyte cell-cell adhesion / response to ATP / response to inorganic substance / calcium ion homeostasis / Purinergic signaling in leishmaniasis infection / side of membrane / ATP metabolic process / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
5'-nucleotidase signature 1. / 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
5'-nucleotidase / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.73 Å
AuthorsZhou, Y.F. / Lord, D.M.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A highly potent CD73 biparatopic antibody blocks organization of the enzyme active site through dual mechanisms.
Authors: Stefano, J.E. / Lord, D.M. / Zhou, Y. / Jaworski, J. / Hopke, J. / Travaline, T. / Zhang, N. / Wong, K. / Lennon, A. / He, T. / Bric-Furlong, E. / Cherrie, C. / Magnay, T. / Remy, E. / ...Authors: Stefano, J.E. / Lord, D.M. / Zhou, Y. / Jaworski, J. / Hopke, J. / Travaline, T. / Zhang, N. / Wong, K. / Lennon, A. / He, T. / Bric-Furlong, E. / Cherrie, C. / Magnay, T. / Remy, E. / Brondyk, W. / Qiu, H. / Radosevic, K.
History
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-nucleotidase, ecto (CD73), isoform CRA_a
B: 5'-nucleotidase, ecto (CD73), isoform CRA_a
C: 5'-nucleotidase, ecto (CD73), isoform CRA_a
D: 5'-nucleotidase, ecto (CD73), isoform CRA_a
H: TB38 heavy chain
L: TB38 light chain
E: TB38 heavy chain
F: TB38 light chain
P: TB38 heavy chain
O: TB38 light chain
K: TB38 heavy chain
J: TB38 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,80615
Polymers427,57312
Non-polymers1,2323
Water0
1
A: 5'-nucleotidase, ecto (CD73), isoform CRA_a
B: 5'-nucleotidase, ecto (CD73), isoform CRA_a
H: TB38 heavy chain
L: TB38 light chain
E: TB38 heavy chain
F: TB38 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,7988
Polymers213,7876
Non-polymers1,0112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-nucleotidase, ecto (CD73), isoform CRA_a
D: 5'-nucleotidase, ecto (CD73), isoform CRA_a
P: TB38 heavy chain
O: TB38 light chain
K: TB38 heavy chain
J: TB38 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,0087
Polymers213,7876
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)236.910, 336.200, 222.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
5'-nucleotidase, ecto (CD73), isoform CRA_a / / Ecto-5'-nucleotidase


Mass: 58882.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, hCG_401111 / Production host: Homo sapiens (human)
References: UniProt: Q53Z63, UniProt: P21589*PLUS, 5'-nucleotidase

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Antibody , 2 types, 8 molecules HEPKLFOJ

#2: Antibody
TB38 heavy chain


Mass: 25160.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
TB38 light chain


Mass: 22850.287 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 3 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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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Details

Has ligand of interestN

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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: 5.17 Å3/Da / Density % sol: 76.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.6M sodium phosphate monobasic monohydrate, 0.4M potassium phosphate dibasic, and 0.1M sodium phosphate citrate pH 5.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.73→78.612 Å / Num. obs: 92120 / % possible obs: 99.9 % / Redundancy: 6.586 % / Biso Wilson estimate: 135.164 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.277 / Χ2: 0.939 / Net I/σ(I): 6.12 / Num. measured all: 606702 / Scaling rejects: 75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.73-3.836.6843.5850.5945232676867670.1943.889100
3.83-3.936.7962.8930.7844583656565600.283.13499.9
3.93-4.056.642.1641.0642447639763930.4172.3599.9
4.05-4.176.9181.6861.4943003621962160.5641.824100
4.17-4.316.8111.311.9341155604860420.6971.41999.9
4.31-4.466.6740.9292.7739019584658460.8191.008100
4.46-4.636.320.6833.5535647564556400.8770.74599.9
4.63-4.826.6740.5764.1736271544054350.9240.62599.9
4.82-5.036.4960.4545.0234066524452440.9420.494100
5.03-5.286.8520.4185.5334128498149810.9460.453100
5.28-5.566.770.3695.9532230476147610.9540.4100
5.56-5.96.6060.3356.2929788451045090.960.364100
5.9-6.36.4160.2697.1927221424342430.9680.293100
6.3-6.816.4650.2118.6425602396239600.980.2399.9
6.81-7.466.7260.14711.7124558365236510.9890.16100
7.46-8.346.410.09715.8521282332433200.9950.10699.9
8.34-9.636.0460.06920.1217823294929480.9960.076100
9.63-11.86.1670.05624.4715466251125080.9970.06199.9
11.8-16.685.7390.05224.7211323197619730.9970.05899.8
16.68-78.6125.2160.05425.035858115311230.9960.0697.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H2F

4h2f


Resolution: 3.73→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 46.313 / SU ML: 0.584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.566
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.264 4586 5 %RANDOM
Rwork0.2238 ---
obs0.2258 87359 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 548.42 Å2 / Biso mean: 180.637 Å2 / Biso min: 59.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å2-0 Å20 Å2
2---6.17 Å2-0 Å2
3---8.62 Å2
Refinement stepCycle: final / Resolution: 3.73→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27730 0 81 0 27811
Biso mean--228.12 --
Num. residues----3616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01328519
X-RAY DIFFRACTIONr_bond_other_d0.0020.01725937
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.64238782
X-RAY DIFFRACTIONr_angle_other_deg1.1741.57660402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.30453613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19223.1421308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.926154630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2515122
X-RAY DIFFRACTIONr_chiral_restr0.0650.23718
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0231967
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025792
LS refinement shellResolution: 3.73→3.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 365 -
Rwork0.392 6279 -
all-6644 -
obs--99.18 %

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