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- PDB-2bde: Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotida... -

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Basic information

Entry
Database: PDB / ID: 2bde
TitleCrystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1
Componentscytosolic IMP-GMP specific 5'-nucleotidase
KeywordsDNA BINDING PROTEIN / alpha beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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
Cytosolic IMP-GMP specific 5'-nucleotidase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsForouhar, F. / Abashidze, M. / Ho, C.K. / Conover, K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1
Authors: Forouhar, F. / Abashidze, M. / Ho, C.K. / Conover, K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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)55,3513
Polymers55,1591
Non-polymers1922
Water1,27971
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)221,40312
Polymers220,6344
Non-polymers7698
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
2
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)110,7016
Polymers110,3172
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+3/2,y,-z+3/41
Buried area2900 Å2
ΔGint-85 kcal/mol
Surface area45050 Å2
MethodPISA
3
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)110,7016
Polymers110,3172
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area6300 Å2
ΔGint-80 kcal/mol
Surface area41660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.540, 152.540, 188.406
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: 55158.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Gene: 3078646 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-Gold+Magic / References: UniProt: Q5ZZB6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 4.97 Å3/Da / Density % sol: 75.23 %
Description: Reflections reported in data collection include friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: 100mM MES, 20% PEG400, 100mM KBr, 5mM DTT, pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898, 0.97943, 0.96795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978981
20.979431
30.967951
ReflectionResolution: 2.9→30.12 Å / Num. all: 44284 / Num. obs: 44284 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.9 % / Biso Wilson estimate: 70.2 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.081 / Net I/σ(I): 29
Reflection shellResolution: 2.9→3 Å / Redundancy: 18.9 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 10.93 / Num. unique all: 2447 / Rsym value: 0.285 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→30.12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 475983.63 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs have been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.267 4327 9.8 %RANDOM
Rwork0.221 ---
all0.224 44284 --
obs0.221 44284 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.9387 Å2 / ksol: 0.302233 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.71 Å20 Å20 Å2
2--4.07 Å20 Å2
3----8.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.9→30.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 10 71 3839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 681 10.3 %
Rwork0.31 5919 -
obs-4327 83.9 %

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