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- PDB-4q7f: 1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from ... -

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Basic information

Entry
Database: PDB / ID: 4q7f
Title1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with Adenosine.
Components5' nucleotidase family protein
KeywordsMETAL BINDING PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / 5'-nucleotidase / C-terminal domain / phosphoesterase / metal ion binding
Function / homology
Function and homology information


nucleotidase activity / nucleotide catabolic process / hydrolase activity, acting on ester bonds / outer membrane-bounded periplasmic space / nucleotide binding / metal ion binding
Similarity search - Function
5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-3D1 / : / Bifunctional metallophosphatase/5'-nucleotidase / 5' nucleotidase family protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMinasov, G. / Nocadello, S. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with Adenosine.
Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_ref_seq_dif / 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_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5' nucleotidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9714
Polymers60,6411
Non-polymers3303
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.584, 86.452, 95.647
Angle α, β, γ (deg.)90.00, 116.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-966-

HOH

21A-1031-

HOH

31A-1075-

HOH

41A-1076-

HOH

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Components

#1: Protein 5' nucleotidase family protein


Mass: 60640.652 Da / Num. of mol.: 1 / Fragment: Putative 5'-Nucleotidase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: SACOL0130, SAOUHSC_00107 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q5HJM3, UniProt: Q2G1L5*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-3D1 / (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol / 2'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Protein: 7.0 mg/mL, 0.5M Sodium chloride, Tris-HCl pH 7.2, 0.5 mM TCEP, 1 mM Adenosine; Screen: PEGs II (D1), 0.1M Sodium acetate, 0.1M Sodium HEPES, 22% (w/v) PEG 4000, VAPOR DIFFUSION, ...Details: Protein: 7.0 mg/mL, 0.5M Sodium chloride, Tris-HCl pH 7.2, 0.5 mM TCEP, 1 mM Adenosine; Screen: PEGs II (D1), 0.1M Sodium acetate, 0.1M Sodium HEPES, 22% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2014 / Details: beryllium lenses
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. all: 44896 / Num. obs: 44896 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 16.7
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2238 / Rsym value: 0.62 / % possible all: 97.2

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3QFK

3qfk


Resolution: 1.98→29.36 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.663 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21788 2236 5 %RANDOM
Rwork0.1869 ---
obs0.18846 42209 97.96 %-
all-42209 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å20.88 Å2
2--5.7 Å20 Å2
3----4.25 Å2
Refinement stepCycle: LAST / Resolution: 1.98→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 20 380 4492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194355
X-RAY DIFFRACTIONr_bond_other_d0.0010.023971
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9545940
X-RAY DIFFRACTIONr_angle_other_deg0.74639136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1165537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56624.786234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.59815669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4161522
X-RAY DIFFRACTIONr_chiral_restr0.0880.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021077
X-RAY DIFFRACTIONr_mcbond_it1.1541.5022109
X-RAY DIFFRACTIONr_mcbond_other1.1541.5022108
X-RAY DIFFRACTIONr_mcangle_it1.8752.252659
X-RAY DIFFRACTIONr_mcangle_other1.8752.252660
X-RAY DIFFRACTIONr_scbond_it1.4231.692246
X-RAY DIFFRACTIONr_scbond_other1.4221.692246
X-RAY DIFFRACTIONr_scangle_other2.2182.4843282
X-RAY DIFFRACTIONr_long_range_B_refined6.30813.6215279
X-RAY DIFFRACTIONr_long_range_B_other6.14313.0115122
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 180 -
Rwork0.326 3073 -
obs-3073 97.08 %
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)
12.46920.5534-0.14870.7461-0.04440.6765-0.17640.016-0.00260.00810.0628-0.08040.02490.00460.11360.10250.08470.02460.08260.01740.0663-33.723131.206299.3925
21.5356-0.3596-0.56420.81610.24011.3497-0.0971-0.29020.23450.11770.1351-0.1603-0.0820.1255-0.0380.12120.1122-0.02190.1476-0.02840.1409-29.6540.1148113.3138
32.1762-0.36520.00510.5510.25211.3021-0.11520.0886-0.1512-0.04120.0097-0.060.0937-0.02810.10550.13370.04970.02910.08240.01480.072-40.834931.061795.8146
40.7954-0.1644-0.53682.16330.74651.1457-0.03140.1386-0.0279-0.09720.05470.17630.0196-0.1705-0.02330.11970.10510.01840.18950.02140.0865-60.943944.3453106.6494
52.097-1.13610.42912.95490.13071.2950.0320.16370.1448-0.03230.0091-0.09830.0370.1061-0.04110.12020.14370.04240.18960.03620.124-57.093559.0973106.2002
61.7170.2871-0.83482.7952-0.18692.4944-0.02970.00490.08080.186-0.09010.18710.0799-0.05620.11980.13240.12650.06130.16890.0210.0997-60.098544.2702117.0322
73.96333.789-1.911911.1925-2.71491.1436-0.29480.44850.2056-0.75950.41951.06470.128-0.3537-0.12470.12650.0765-0.08460.2506-0.030.1903-70.487848.9161102.4288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 69
2X-RAY DIFFRACTION2A70 - 263
3X-RAY DIFFRACTION3A264 - 315
4X-RAY DIFFRACTION4A316 - 389
5X-RAY DIFFRACTION5A390 - 449
6X-RAY DIFFRACTION6A450 - 495
7X-RAY DIFFRACTION7A496 - 511

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