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- PDB-4g63: Crystal structure of cytosolic IMP-GMP specific 5'-nucleotidase (... -

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Basic information

Entry
Database: PDB / ID: 4g63
TitleCrystal structure of cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) in complex with phosphate ions from Legionella pneumophila, Northeast Structural Genomics Consortium Target LgR1
ComponentsCytosolic IMP-GMP specific 5'-nucleotidase
KeywordsDNA BINDING PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / alpha-beta protein / HAD-like superfamily
Function / homology
Function and homology information


hydrolase 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
PHOSPHATE ION / Cytosolic IMP-GMP specific 5'-nucleotidase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Ho, C.K. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / 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
DepositionJul 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references / Derived calculations
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Sep 13, 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 / 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 / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,9263
Polymers54,7361
Non-polymers1902
Water1,60389
1
A: Cytosolic IMP-GMP specific 5'-nucleotidase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)219,70612
Polymers218,9464
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Unit cell
Length a, b, c (Å)154.089, 154.089, 191.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 54736.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg0095 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5ZZB6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 5.212 Å3/Da / Density % sol: 75.955 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM MES (pH 6.15), 20 % (w/v) PEG400, and 100 mM KBr, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 31858 / Num. obs: 31731 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 60.1 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.062 / Net I/σ(I): 30.54
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 6.12 / Num. unique all: 3130 / Rsym value: 0.493 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
COMOphasing
CNS1.3 & XtalViewrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BDE

2bde


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 384136.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2920 10 %RANDOM
Rwork0.222 ---
all0.225 31772 --
obs0.222 29199 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1622 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 61.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.02 Å20 Å20 Å2
2--6.02 Å20 Å2
3----12.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 0 10 89 3824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 411 9.9 %
Rwork0.282 3735 -
obs-3735 79.5 %

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