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- PDB-4nv0: Crystal structure of cytosolic 5'-nucleotidase IIIB (cN-IIIB) bou... -

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Basic information

Entry
Database: PDB / ID: 4nv0
TitleCrystal structure of cytosolic 5'-nucleotidase IIIB (cN-IIIB) bound to 7-methylguanosine
Components7-methylguanosine phosphate-specific 5'-nucleotidase
KeywordsHYDROLASE / Rossmannoid fold / 5'-Nucleotidase
Function / homology
Function and homology information


ribonucleoside monophosphate catabolic process / guanosine-containing compound catabolic process / mRNA decay by 3' to 5' exoribonuclease / Pyrimidine catabolism / nucleotidase activity / 7-methylguanosine nucleotidase / : / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process ...ribonucleoside monophosphate catabolic process / guanosine-containing compound catabolic process / mRNA decay by 3' to 5' exoribonuclease / Pyrimidine catabolism / nucleotidase activity / 7-methylguanosine nucleotidase / : / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process / nucleotide binding / magnesium ion binding / cytosol / cytoplasm
Similarity search - Function
Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain / Pyrimidine 5'-nucleotidase, eukaryotic / Pyrimidine 5'-nucleotidase (UMPH-1) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain / Pyrimidine 5'-nucleotidase, eukaryotic / Pyrimidine 5'-nucleotidase (UMPH-1) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
7-METHYLGUANOSINE / TRIFLUOROMAGNESATE / TRIETHYLENE GLYCOL / 7-methylguanosine phosphate-specific 5'-nucleotidase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMonecke, T. / Neumann, P. / Ficner, R.
CitationJournal: Plos One / Year: 2014
Title: Crystal Structures of the Novel Cytosolic 5'-Nucleotidase IIIB Explain Its Preference for m7GMP
Authors: Monecke, T. / Buschmann, J. / Neumann, P. / Wahle, E. / Ficner, R.
History
DepositionDec 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7-methylguanosine phosphate-specific 5'-nucleotidase
B: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6349
Polymers72,6762
Non-polymers9587
Water10,503583
1
A: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8925
Polymers36,3381
Non-polymers5544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7424
Polymers36,3381
Non-polymers4043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.670, 99.110, 74.120
Angle α, β, γ (deg.)90.00, 90.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 7-methylguanosine phosphate-specific 5'-nucleotidase / cytosolic 5'-nucleotidase IIIB / 5'-nucleotidase CG3362


Mass: 36338.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3362 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE2) / References: UniProt: Q9W197, 5'-nucleotidase

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Non-polymers , 5 types, 590 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MG7 / 7-METHYLGUANOSINE


Mass: 298.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N5O5
#5: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F3Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 26% PEG 4000, 0.1M HEPES, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 19, 2012
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.65→46.67 Å / Num. all: 80943 / Num. obs: 76459 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.5
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.17 / % possible all: 81.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G08

2g08


Resolution: 1.65→41.194 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.8833 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 3823 5 %RANDOM
Rwork0.1591 ---
all0.1608 76416 --
obs0.1608 76416 94.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.6 Å2 / Biso mean: 21.442 Å2 / Biso min: 6.23 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4813 0 62 583 5458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115189
X-RAY DIFFRACTIONf_angle_d1.587051
X-RAY DIFFRACTIONf_chiral_restr0.212770
X-RAY DIFFRACTIONf_plane_restr0.006923
X-RAY DIFFRACTIONf_dihedral_angle_d14.3251947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.67090.28721180.25232234235278
1.6709-1.69290.30321210.24532287240881
1.6929-1.71610.26051220.23942327244982
1.7161-1.74060.26781260.23092390251684
1.7406-1.76660.2721310.22252490262187
1.7666-1.79420.2481390.21362642278193
1.7942-1.82360.23431430.1982706284997
1.8236-1.8550.19781460.17872768291496
1.855-1.88880.21481430.17552717286097
1.8888-1.92510.21131440.16022752289697
1.9251-1.96440.17791440.15642730287497
1.9644-2.00710.21671460.1592770291697
2.0071-2.05380.20561440.16252744288897
2.0538-2.10520.20511460.15812768291497
2.1052-2.16210.1881450.15422760290597
2.1621-2.22570.2071470.15112784293197
2.2257-2.29750.17531450.14692747289298
2.2975-2.37960.18891460.14762788293498
2.3796-2.47490.18641470.15482789293698
2.4749-2.58750.18621450.15342757290298
2.5875-2.72390.19831470.16132787293498
2.7239-2.89450.21921480.16242809295798
2.8945-3.11790.20131480.16492805295398
3.1179-3.43160.19731460.15752783292998
3.4316-3.92780.17341490.13782816296598
3.9278-4.94730.14041470.12132800294797
4.9473-41.20680.17561500.16112843299398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9658-0.58982.17512.0992-0.76984.037-0.06420.06030.1355-0.00570.0163-0.1346-0.3899-0.024-0.00770.1632-0.00150.00150.1213-0.00150.1568-12.71639.086612.6218
20.686-0.1418-0.15151.10640.31560.7269-0.0168-0.03820.07-0.02690.02010.0177-0.0449-0.04880.01690.06280.0055-0.00640.0998-0.0040.079-17.2093-3.775310.1894
32.6860.75450.83382.57660.54952.0222-0.05970.0571-0.2691-0.59690.1729-0.3501-0.10440.3834-0.1330.2229-0.02820.10360.1944-0.02610.1463-6.633-15.9501-14.7771
41.2283-0.6228-0.03942.52350.04410.9460.30750.38360.0857-0.6314-0.3634-0.1113-0.3059-0.25330.01340.31820.10080.00780.21040.02180.1975-23.1071-9.6662-18.9162
51.52691.25571.73971.42371.60292.11340.06480.138-0.1901-0.00170.0868-0.16530.10820.3384-0.07520.17740.01450.04110.2148-0.04080.2086-7.0175-23.1025-11.0391
60.3415-0.0458-0.33060.91370.66751.35890.00450.0311-0.0942-0.0272-0.07620.06070.0447-0.1160.05980.096-0.00250.00670.0903-0.00630.1013-18.9567-15.31852.305
71.6339-0.2530.07071.32740.66241.10710.09830.03350.1447-0.1055-0.03160.0002-0.1669-0.0135-0.04560.09980.00610.01120.07990.00830.0951-14.14130.65977.6881
81.90050.539-1.12121.9864-0.47264.0411-0.16650.0012-0.1519-0.00510.104-0.09810.407-0.04130.03990.14330.01390.0040.1504-0.01520.1681-34.7116-13.7204-49.587
90.35690.1203-0.15971.01480.42120.4442-0.02680.0118-0.06770.05640.05280.00080.0569-0.0607-0.04040.07140.00190.00580.1047-0.00970.0823-38.5115-0.9351-45.8463
101.1157-0.6115-1.04721.82380.41661.3367-0.0217-0.26930.12930.43290.1215-0.52420.11050.4489-0.07090.18750.0539-0.07710.2446-0.03170.2053-27.28069.5131-24.655
111.3920.1511-0.10522.0665-0.34581.3249-0.1547-0.1012-0.06930.44080.09040.08990.0841-0.15790.03150.3216-0.01390.05730.2179-0.00210.143-42.39445.4235-17.0755
120.5199-0.3525-0.36230.92570.1871.21220.0107-0.08120.21150.10130.0581-0.1828-0.11810.2133-0.04570.0968-0.0147-0.00810.121-0.04080.1418-32.324713.8979-36.6417
130.82191.88380.85484.30481.95990.89270.0308-0.0960.3070.4295-0.17680.5280.0036-0.21720.13330.17060.00190.0260.1347-0.04480.1854-45.838216.7667-27.1041
140.84760.06380.43090.49580.17241.3784-0.0177-0.14130.15430.0474-0.04480.2041-0.0327-0.1790.0390.08610.00240.0070.1408-0.03270.1412-48.74096.5469-43.7024
151.4445-0.10430.39061.8201-0.95543.17390.0631-0.1606-0.16030.349-0.07840.13010.2950.1610.00450.2-0.00790.03060.14320.01230.1137-40.0168-9.1485-35.7634
161.64770.21860.00021.5930.19721.48360.04030.13970.0137-0.16460.0066-0.06750.00440.0895-0.00550.10990.01010.00850.1095-0.01780.0944-33.0209-1.9297-51.5054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 13 THROUGH 31 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 32 THROUGH 64 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 65 THROUGH 87 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 88 THROUGH 127 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 128 THROUGH 148 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 149 THROUGH 260 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 261 THROUGH 311 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 13 THROUGH 31 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 32 THROUGH 64 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 65 THROUGH 85 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 86 THROUGH 127 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 128 THROUGH 200 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 201 THROUGH 220 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 221 THROUGH 260 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 261 THROUGH 282 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 283 THROUGH 312 )

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