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- PDB-1k9y: The PAPase Hal2p complexed with magnesium ions and reaction produ... -

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Basic information

Entry
Database: PDB / ID: 1k9y
TitleThe PAPase Hal2p complexed with magnesium ions and reaction products: AMP and inorganic phosphate
ComponentsHalotolerance protein HAL2
KeywordsHYDROLASE / NUCLEOTIDASE / SALT TOLERANCE / INOSITOL
Function / homology
Function and homology information


3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / hyperosmotic salinity response / sulfate assimilation / tRNA decay / methionine biosynthetic process / phosphatidylinositol phosphate biosynthetic process / metal ion binding / nucleus / cytoplasm
Similarity search - Function
3(2),5 -bisphosphate nucleotidase HAL2 / : / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...3(2),5 -bisphosphate nucleotidase HAL2 / : / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BETA-MERCAPTOETHANOL / PHOSPHATE ION / 3'(2'),5'-bisphosphate nucleotidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPatel, S. / Albert, A. / Blundell, T.L.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural enzymology of Li(+)-sensitive/Mg(2+)-dependent phosphatases.
Authors: Patel, S. / Martinez-Ripoll, M. / Blundell, T.L. / Albert, A.
History
DepositionOct 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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.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_conn.ptnr2_label_seq_id / _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: Halotolerance protein HAL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7927
Polymers39,1991
Non-polymers5936
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.693, 45.075, 71.794
Angle α, β, γ (deg.)90.00, 110.96, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Halotolerance protein HAL2 / HAL2p / 3'(2') / 5'-Bisphosphate nucleotidase / Phosphoadenylate 3'-nucleotidase / 3'- ...HAL2p / 3'(2') / 5'-Bisphosphate nucleotidase / Phosphoadenylate 3'-nucleotidase / 3'-Phosphoadenylylsulfate 3'-phosphatase


Mass: 39199.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HAL2 / Plasmid: pRS-421-HAL2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): RS1051
References: UniProt: P32179, 3'(2'),5'-bisphosphate nucleotidase

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Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 % PEG5000 MME, 0.1 M sodium acetate, 5 mM beta-mercaptoethanol, 0.1 M MES (Crystals were soaked in mother liquor containing 1 M magnesium chloride for 1 hour), pH 6.5, VAPOR DIFFUSION, ...Details: 30 % PEG5000 MME, 0.1 M sodium acetate, 5 mM beta-mercaptoethanol, 0.1 M MES (Crystals were soaked in mother liquor containing 1 M magnesium chloride for 1 hour), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Msodium acetate1drop
20.1 MMES1drop
35 mMbeta-mercaptoethanol1drop
430 %(w/v)PEG5000 MME1drop
50.56 mMprotein1drop
61 M1reservoiror 0.5M CaCl2MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 8, 1999
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→67.42 Å / Num. all: 25897 / Num. obs: 25897 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.949 Å / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGX

1qgx


Resolution: 1.9→67.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.784 / SU ML: 0.142 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20348 1306 5 %RANDOM
Rwork0.1559 ---
obs0.15845 25847 99.43 %-
all-25847 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.369 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å2-0.42 Å2
2--1.47 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 35 235 2997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212805
X-RAY DIFFRACTIONr_bond_other_d00.022514
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9653798
X-RAY DIFFRACTIONr_angle_other_deg0.8335866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3463353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56615501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023124
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02542
X-RAY DIFFRACTIONr_nbd_refined0.2350.3621
X-RAY DIFFRACTIONr_nbd_other0.2190.32436
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5245
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.51
X-RAY DIFFRACTIONr_metal_ion_refined0.010.53
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3490.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7111.51750
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.65622812
X-RAY DIFFRACTIONr_scbond_it3.98231055
X-RAY DIFFRACTIONr_scangle_it5.9334.5986
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 87 -
Rwork0.243 1824 -
obs--99.5 %
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Lowest resolution: 20 Å / Rfactor obs: 0.151 / Rfactor Rfree: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3.2
X-RAY DIFFRACTIONp_plane_restr0.008
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.345 / Rfactor Rwork: 0.243

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