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- PDB-7d0v: Crystal structure of Taiwan cobra 5'-nucleotidase -

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Basic information

Entry
Database: PDB / ID: 7d0v
TitleCrystal structure of Taiwan cobra 5'-nucleotidase
ComponentsSnake venom 5'-nucleotidase
KeywordsHYDROLASE / 5'-nucleotidase / Cobra Venom / CD73
Function / homology5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / 4-Layer Sandwich / Alpha-Beta Complex / Alpha Beta
Function and homology information
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.175 Å
AuthorsTsai, M.-H. / Lin, I.-J. / Lin, C.-C. / Wu, W.-G.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal structure of Taiwan cobra 5'-nucleotidase
Authors: Tsai, M.-H. / Lin, I.-J. / Lin, C.-C. / Wu, W.-G.
History
DepositionSep 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Snake venom 5'-nucleotidase
B: Snake venom 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,95412
Polymers116,8512
Non-polymers2,10310
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-162 kcal/mol
Surface area41360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.327, 68.127, 140.214
Angle α, β, γ (deg.)90.000, 95.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Snake venom 5'-nucleotidase


Mass: 58425.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: 5'-nucleotidase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 3 types, 544 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 25% PEG 3350, 0.2M Magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.175→30 Å / Num. obs: 52203 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.96
Reflection shellResolution: 2.175→2.26 Å / Rmerge(I) obs: 0.588 / Num. unique obs: 4804

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Processing

Software
NameVersionClassification
PHENIX1.16-3549-000refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H1S

4h1s


Resolution: 2.175→28.67 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2186 2565 -
obs0.1775 52203 98.73 %
Displacement parametersBiso mean: 35.08 Å2
Refinement stepCycle: LAST / Resolution: 2.175→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8150 0 122 538 8810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00658430
X-RAY DIFFRACTIONf_angle_d0.858411402
X-RAY DIFFRACTIONf_chiral_restr0.05541286
X-RAY DIFFRACTIONf_plane_restr0.00591478
X-RAY DIFFRACTIONf_dihedral_angle_d14.61265063
LS refinement shellResolution: 2.175→2.253 Å
RfactorNum. reflection% reflection
Rfree0.2748 --
Rwork0.2239 --
obs-4805 91.4 %

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