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- PDB-4ohf: Crystal structure of cytosolic nucleotidase II (LPG0095) in compl... -

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Basic information

Entry
Database: PDB / ID: 4ohf
TitleCrystal structure of cytosolic nucleotidase II (LPG0095) in complex with GMP from Legionella pneumophila, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET LGR1
ComponentsCytosolic IMP-GMP specific 5'-nucleotidase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / 3-domained structure that resembles HAD / nucleotidase. It catalyzes the breakdown of selected nucleoside monophosphates / cytosol
Function / homology
Function and homology information


5'-nucleotidase activity / identical protein binding / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1160 / HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase / Purine 5'-nucleotidase / 5' nucleotidase family / HAD superfamily/HAD-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / HAD superfamily / HAD-like superfamily / Up-down Bundle / Rossmann fold ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1160 / HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase / Purine 5'-nucleotidase / 5' nucleotidase family / HAD superfamily/HAD-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / HAD superfamily / HAD-like superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / PHOSPHATE ION / Cytosolic IMP-GMP specific 5'-nucleotidase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSrinivisan, B. / Forouhar, F. / Shukla, A. / Sampangi, C. / Kulkarni, S. / Abashidze, M. / Seetharaman, J. / Lew, S. / Mao, L. / Acton, T.B. ...Srinivisan, B. / Forouhar, F. / Shukla, A. / Sampangi, C. / Kulkarni, S. / Abashidze, M. / Seetharaman, J. / Lew, S. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.M. / Tong, L. / Balaram, H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Febs J. / Year: 2014
Title: Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila.
Authors: Srinivasan, B. / Forouhar, F. / Shukla, A. / Sampangi, C. / Kulkarni, S. / Abashidze, M. / Seetharaman, J. / Lew, S. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Balaram, H.
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Structure summary
Revision 1.2Apr 9, 2014Group: Database references
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _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 IMP-GMP specific 5'-nucleotidase
B: Cytosolic IMP-GMP specific 5'-nucleotidase
C: Cytosolic IMP-GMP specific 5'-nucleotidase
D: Cytosolic IMP-GMP specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,50517
Polymers218,9464
Non-polymers1,55913
Water4,107228
1
A: Cytosolic IMP-GMP specific 5'-nucleotidase
B: Cytosolic IMP-GMP specific 5'-nucleotidase
hetero molecules

A: Cytosolic IMP-GMP specific 5'-nucleotidase
B: Cytosolic IMP-GMP specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,48116
Polymers218,9464
Non-polymers1,53512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
A: Cytosolic IMP-GMP specific 5'-nucleotidase
B: Cytosolic IMP-GMP specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2408
Polymers109,4732
Non-polymers7676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-63 kcal/mol
Surface area40200 Å2
MethodPISA
3
C: Cytosolic IMP-GMP specific 5'-nucleotidase
D: Cytosolic IMP-GMP specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2659
Polymers109,4732
Non-polymers7927
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-62 kcal/mol
Surface area39410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.334, 92.720, 161.892
Angle α, β, γ (deg.)90.00, 96.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cytosolic IMP-GMP specific 5'-nucleotidase


Mass: 54736.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg0095 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5ZZB6
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris HCl, pH 5.5, 0.2M ammonium acetate, 25 % w/v PEG3350, and 5 mM GMP-PNP., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 7, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. all: 76798 / Num. obs: 76184 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.075 / Net I/σ(I): 29.57
Reflection shellResolution: 2.53→2.57 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.09 / Num. unique all: 3834 / Rsym value: 0.38 / % possible all: 92

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Processing

Software
NameVersionClassification
CNS1.3refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G63

4g63


Resolution: 2.53→44.7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 199674.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 6753 9.5 %RANDOM
Rwork0.231 ---
all0.233 76798 --
obs0.231 71361 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.0161 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 60.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å2-3.49 Å2
2--3.77 Å20 Å2
3----5.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.53→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14824 0 91 228 15143
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.53→2.69 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 577 5.6 %
Rwork0.336 9641 -
obs-9641 80.3 %

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