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- PDB-7cba: Crystal structure of snake venom phosphodiesterase (PDE) from Tai... -

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Basic information

Entry
Database: PDB / ID: 7cba
TitleCrystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with isorhamnetin and citrate
ComponentsVenom phosphodiesterase
KeywordsHYDROLASE / ATP-hydrolysis glycoprotein enpp inhibitor
Function / homology
Function and homology information


ADP phosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / toxin activity / nucleic acid binding / extracellular region / metal ion binding
Similarity search - Function
Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease ...Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
CITRIC ACID / isorhamnetin / Venom phosphodiesterase
Similarity search - Component
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.901 Å
AuthorsLin, I.J. / Lin, C.C. / Wu, W.G.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)107-2311-B-007 -012 Taiwan
CitationJournal: To Be Published
Title: Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with isorhamnetin and citrate
Authors: Lin, I.J. / Lin, C.C. / Wu, W.G.
History
DepositionJun 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Venom phosphodiesterase
B: Venom phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,53821
Polymers189,4582
Non-polymers4,08019
Water00
1
A: Venom phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,87911
Polymers94,7291
Non-polymers2,15110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-0 kcal/mol
Surface area32330 Å2
MethodPISA
2
B: Venom phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,65810
Polymers94,7291
Non-polymers1,9299
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-3 kcal/mol
Surface area32060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.186, 168.619, 93.715
Angle α, β, γ (deg.)90.000, 105.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 67 through 125 or resid 131...
21(chain B and (resid 67 through 453 or resid 457...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 67 through 125 or resid 131...A67 - 125
121(chain A and (resid 67 through 125 or resid 131...A131 - 626
131(chain A and (resid 67 through 125 or resid 131...A639 - 850
141(chain A and (resid 67 through 125 or resid 131...A861 - 862
151(chain A and (resid 67 through 125 or resid 131...A865 - 866
211(chain B and (resid 67 through 453 or resid 457...B67 - 453
221(chain B and (resid 67 through 453 or resid 457...B457 - 850
231(chain B and (resid 67 through 453 or resid 457...B852 - 853
241(chain B and (resid 67 through 453 or resid 457...B857 - 858

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Venom phosphodiesterase / PDE


Mass: 94728.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra)
References: UniProt: A0A2D0TC04, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Sugars , 2 types, 9 molecules

#2: 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
#3: 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.: 7
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 , 4 types, 10 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-IRH / isorhamnetin / 3,5,7-trihydroxy-2-(4-hydroxy-3-methoxyphenyl)-4H-1-benzopyran-4-one


Mass: 316.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12O7 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION

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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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 42715 / % possible obs: 97.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.059 / Rrim(I) all: 0.112 / Χ2: 0.851 / Net I/σ(I): 7.4 / Num. measured all: 153134
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-32.90.46538040.7760.3140.5640.80187.2
3-3.123.30.38641510.8550.2480.4610.82995.5
3.12-3.273.50.29742460.9050.1830.350.89198.2
3.27-3.443.70.21943400.9510.1330.2570.91399.6
3.44-3.653.80.16343710.9720.0970.190.93100
3.65-3.933.80.11543660.9840.0680.1340.899100
3.93-4.333.80.08443470.990.050.0980.91399.9
4.33-4.953.70.05743620.9940.0350.0670.87799.8
4.95-6.233.80.05143850.9940.0310.060.758100
6.23-303.50.02743430.9970.0170.0320.66698.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14-3260phasing
RefinementMethod to determine structure: MIR / Resolution: 2.901→28.296 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 2141 5.26 %
Rwork0.1874 38550 -
obs0.1903 40691 93.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.14 Å2 / Biso mean: 48.2364 Å2 / Biso min: 17.65 Å2
Refinement stepCycle: final / Resolution: 2.901→28.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12322 0 254 0 12576
Biso mean--59.5 --
Num. residues----1536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4660X-RAY DIFFRACTION6.034TORSIONAL
12B4660X-RAY DIFFRACTION6.034TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.901-2.96790.3283870.2762177764
2.9679-3.04210.32741080.2657204975
3.0421-3.12420.31851050.2669231983
3.1242-3.2160.32791560.2584239689
3.216-3.31970.30351700.2408257894
3.3197-3.43810.28151490.2247265397
3.4381-3.57550.30781390.22262753100
3.5755-3.73790.27941620.19612736100
3.7379-3.93450.2261580.18092774100
3.9345-4.18030.25261360.16972743100
4.1803-4.50180.20051590.15792766100
4.5018-4.95270.20861470.1432762100
4.9527-5.66440.21351640.1622740100
5.6644-7.11770.20681550.17422771100
7.1177-28.2960.18681460.1621273397

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