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- PDB-2xcv: Crystal structure of the D52N variant of cytosolic 5'-nucleotidas... -

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Basic information

Entry
Database: PDB / ID: 2xcv
TitleCrystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inosine monophosphate and 2,3-bisphosphoglycerate
ComponentsCYTOSOLIC PURINE 5'-NUCLEOTIDASE
KeywordsHYDROLASE / METAL-BINDING / NUCLEOTIDE METABOLISM
Function / homology
Function and homology information


nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / GMP metabolic process / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / adenosine metabolic process / amide catabolic process ...nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / GMP metabolic process / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / adenosine metabolic process / amide catabolic process / : / dGMP catabolic process / IMP-specific 5'-nucleotidase / : / IMP catabolic process / Ribavirin ADME / IMP metabolic process / Purine catabolism / 5'-nucleotidase / allantoin metabolic process / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase / Purine 5'-nucleotidase / 5' nucleotidase family / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
(2R)-2,3-diphosphoglyceric acid / INOSINIC ACID / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWallden, K. / Nordlund, P.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Basis for the Allosteric Regulation and Substrate Recognition of Human Cytosolic 5'-Nucleotidase II
Authors: Wallden, K. / Nordlund, P.
History
DepositionApr 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Non-polymer description / Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_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: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6875
Polymers63,9571
Non-polymers7314
Water4,648258
1
A: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules

A: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules

A: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules

A: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,75020
Polymers255,8274
Non-polymers2,92316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation2_555-x,-y,z1
Buried area15620 Å2
ΔGint-101.8 kcal/mol
Surface area74170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.570, 127.790, 130.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYTOSOLIC PURINE 5'-NUCLEOTIDASE / CYTOSOLIC 5'-NUCLEOTIDASE II


Mass: 63956.750 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE2 / References: UniProt: P49902, 5'-nucleotidase

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-DG2 / (2R)-2,3-diphosphoglyceric acid / 2,3-Bisphosphoglyceric acid / 2,3-bisphosphoglycerate / 2,3-BPG / 2,3-diphosphoglyceric acid / 2,3-diphosphoglycerate / 2,3-DPG / (2~{R})-2,3-diphosphonooxypropanoic acid


Mass: 266.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O10P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 52 TO ASN

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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: 3.16 Å3/Da / Density % sol: 61 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0081
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2008 / Details: DYNAMICALLY BENDABLE
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0081 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 34216 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JCM

2jcm


Resolution: 2.3→48.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.283 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22868 1729 5.1 %RANDOM
Rwork0.17627 ---
obs0.17893 32486 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.669 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20 Å2
2--1.08 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 45 258 4070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224025
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9735452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15822.812192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82315699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4391530
X-RAY DIFFRACTIONr_chiral_restr0.1260.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023081
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21717
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22742
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2181.52436
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02123821
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.05931830
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.414.51631
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 126 -
Rwork0.223 2364 -
obs--99.2 %

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