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- PDB-2xcx: Crystal structure of the apoform of the D52N variant of cytosolic... -

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Basic information

Entry
Database: PDB / ID: 2xcx
TitleCrystal structure of the apoform of the D52N variant of cytosolic 5'- nucleotidase II
ComponentsCYTOSOLIC PURINE 5'-NUCLEOTIDASE
KeywordsHYDROLASE / CN-II / GMP-IMP SPECIFIC NUCLEOTIDASE / HIGH KM 5-PRIME NUCLEOTIDASE / METAL-BINDING / NT5C2 / NUCLEOTIDE METABOLISM / NUCLEOTIDE-BINDING
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 / dGMP catabolic process / adenosine metabolic 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 / dGMP catabolic process / adenosine metabolic process / : / amide 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
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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / 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 / _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)64,3255
Polymers63,9571
Non-polymers3684
Water4,252236
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)257,30120
Polymers255,8274
Non-polymers1,47416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area17650 Å2
ΔGint-71.3 kcal/mol
Surface area76820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.120, 126.510, 130.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 63956.750 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-536 / 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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
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
Crystal growDetails: 0.1 M BICINE PH9.0, 10% PEG6000

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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: 34076 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.37
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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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: 0.931 / SU B: 11.728 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22901 1727 5.1 %RANDOM
Rwork0.18234 ---
obs0.18476 32347 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2--0.74 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 24 236 4065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223975
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9615370
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6315474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49823.105190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10915679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1371525
X-RAY DIFFRACTIONr_chiral_restr0.1060.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023027
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21702
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22691
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7961.52416
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32623792
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.19231793
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1834.51578
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
Rfree0.339 138
Rwork0.258 2347
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)
110.11688.7602-7.214513.0392-2.11268.2792-0.7667-0.0444-1.3144-1.34290.2677-0.04231.4809-0.07460.4990.6882-0.0159-0.13240.42160.16980.5441-9.097-41.428-25.733
21.92580.54080.19081.0704-0.22480.59250.0174-0.0681-0.0004-0.0128-0.0002-0.10430.1290.0208-0.01720.12880.00710.0036-0.2401-0.0287-0.09046.079-21.854-21.742
31.8071-6.74290.723927.09416.238641.6029-0.0813-0.8685-0.02132.2629-0.7315-2.4414.10062.27550.81280.46820.0118-0.00610.64610.07760.495626.919-23.74-9.978
42.89420.88070.2592.2322-0.21460.8852-0.04520.02660.21010.09630.006-0.2067-0.0830.08130.03920.11380.03120.0273-0.2203-0.0296-0.012312.507-13.838-23.302
51.61820.34090.39142.76840.61361.8775-0.0198-0.06760.08570.05760.00950.10320.0147-0.09210.01030.0589-0.0242-0.0446-0.2097-0.0063-0.052-17.734-19.465-26.749
61.6206-0.1131-0.06359.8631-5.06514.227-0.3526-0.16750.08660.31210.43850.8175-0.0492-0.6049-0.08590.1217-0.01930.0135-0.0683-0.08010.1669-23.156-9.991-20.951
76.2569-1.28380.25684.0883-1.70661.9638-0.0442-0.0741-0.4099-0.1905-0.2159-0.29930.31870.12430.26010.1893-0.03490.0252-0.16010.0101-0.0757-1.923-31.516-16.161
81.3953-1.63261.67793.5172-3.680129.3862-0.22440.27830.0450.1482-0.2813-0.44152.04792.25380.50570.53060.31220.1370.02210.06740.38820.439-41.948-4.111
95.08060.68810.38072.6656-0.11211.20830.0882-0.3032-0.113-0.0528-0.0766-0.02210.2509-0.0705-0.01170.19760.0098-0.019-0.19680.0209-0.1401-1.826-32.056-13.906
1010.64860.011916.445300.018425.39770.39070.0355-0.3846-0.2160.39910.07850.9266-0.0228-0.78970.5554-0.0498-0.09580.1083-0.01080.206-6.601-38.2512.361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 32
2X-RAY DIFFRACTION2A33 - 126
3X-RAY DIFFRACTION3A127 - 136
4X-RAY DIFFRACTION4A137 - 231
5X-RAY DIFFRACTION5A232 - 305
6X-RAY DIFFRACTION6A306 - 345
7X-RAY DIFFRACTION7A346 - 389
8X-RAY DIFFRACTION8A390 - 432
9X-RAY DIFFRACTION9A433 - 475
10X-RAY DIFFRACTION10A476 - 488

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