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- PDB-1g5b: BACTERIOPHAGE LAMBDA SER/THR PROTEIN PHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1g5b
TitleBACTERIOPHAGE LAMBDA SER/THR PROTEIN PHOSPHATASE
ComponentsSERINE/THREONINE PROTEIN PHOSPHATASE
KeywordsViral protein / hydrolase / Bacteriophage Lambda / Ser/Thr Protein Phosphatase / PPase / Protein Phosphatase / Manganese / Sulfate
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / RNA decapping / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / metal ion binding
Similarity search - Function
: / Serine/threonine specific protein phosphatases signature. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / 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
Similarity search - Domain/homology
: / : / Serine/threonine-protein phosphatase
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsVoegtli, W.C. / White, D.J. / Reiter, N.J. / Rusnak, F. / Rosenzweig, A.C.
CitationJournal: Biochemistry / Year: 2000
Title: Structure of the bacteriophage lambda Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes.
Authors: Voegtli, W.C. / White, D.J. / Reiter, N.J. / Rusnak, F. / Rosenzweig, A.C.
History
DepositionOct 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: SERINE/THREONINE PROTEIN PHOSPHATASE
B: SERINE/THREONINE PROTEIN PHOSPHATASE
C: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,69015
Polymers75,5753
Non-polymers1,11512
Water5,495305
1
A: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5985
Polymers25,1921
Non-polymers4074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6946
Polymers25,1921
Non-polymers5035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3984
Polymers25,1921
Non-polymers2063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules

B: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules

C: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules

C: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,18420
Polymers100,7674
Non-polymers1,41716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Buried area7880 Å2
ΔGint-236 kcal/mol
Surface area37880 Å2
MethodPISA
5
B: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules

C: SERINE/THREONINE PROTEIN PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,09210
Polymers50,3832
Non-polymers7098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
Buried area2790 Å2
ΔGint-112 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.400, 177.300, 79.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsBiological assembly is a monomer

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Components

#1: Protein SERINE/THREONINE PROTEIN PHOSPHATASE


Mass: 25191.723 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P03772, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3.72 Å3/Da / Density % sol: 66.93 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, 20% PEG 4000, 350 mM Ammonium Sulfate, 10 mM Manganese(II) Chloride, 50 mM Ammonium Acetate, 20 mM Dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 23K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
119-30 mg/mlprotein1drop
2100 mMMES1reservoirpH6.0
3350 mMammonium sulfate1reservoir
420 %PEG40001reservoir
5100 mMammonium acetate1reservoir
610 mM1reservoirMnCl2
720 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.99188, 1.0098, 1.0247
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 1999
RadiationMonochromator: Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.991881
21.00981
31.02471
ReflectionResolution: 2.15→30 Å / Num. all: 61694 / Num. obs: 61405 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.6
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 435477
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 250651.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2842 4.9 %RANDOM
Rwork0.2 ---
all0.2 61605 --
obs0.2 57583 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.65 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-20 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.15→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5315 0 28 305 5648
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it3.011.5
X-RAY DIFFRACTIONc_mcangle_it4.682
X-RAY DIFFRACTIONc_scbond_it5.272
X-RAY DIFFRACTIONc_scangle_it8.052.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 455 5 %
Rwork0.249 8555 -
obs--88.7 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.268 / % reflection Rfree: 5 % / Rfactor Rwork: 0.249

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