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- PDB-1ka1: The PAPase Hal2p complexed with calcium and magnesium ions and re... -

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Basic information

Entry
Database: PDB / ID: 1ka1
TitleThe PAPase Hal2p complexed with calcium and magnesium ions and reaction substrate: PAP
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 / tRNA decay / sulfate assimilation / methionine biosynthetic process / phosphatidylinositol phosphate biosynthetic process / nucleus / metal ion binding / 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-3'-5'-DIPHOSPHATE / BETA-MERCAPTOETHANOL / 3'(2'),5'-bisphosphate nucleotidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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.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)39,7695
Polymers39,1991
Non-polymers5704
Water8,035446
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.875, 44.968, 72.110
Angle α, β, γ (deg.)90.00, 110.72, 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, 450 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#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.: 446 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
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 0.5 M calcium chloride for 5 hours.) , 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 0.5 M calcium chloride for 5 hours.) , 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: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 1999
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.3→50.31 Å / Num. all: 73179 / Num. obs: 73179 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 1.3→1.334 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 77.1
Reflection shell
*PLUS
% possible obs: 77 %

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Processing

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

1qgx


Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.072 / SU ML: 0.047
Isotropic thermal model: protein and ligands were treated anisotropically while the solvent was isotropic
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1693 3654 5 %RANDOM
Rwork0.13261 ---
obs0.13445 73179 90.28 %-
all-73179 --
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: 12.132 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.27 Å2
2--0.22 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 33 448 3200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212797
X-RAY DIFFRACTIONr_bond_other_d00.022504
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9533789
X-RAY DIFFRACTIONr_angle_other_deg1.2532.9955838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1813353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12315494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023124
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02547
X-RAY DIFFRACTIONr_nbd_refined0.2690.3596
X-RAY DIFFRACTIONr_nbd_other0.2250.32337
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.3830.56
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.5313
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2960.53
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.57
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.528
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3991.51748
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.21422807
X-RAY DIFFRACTIONr_scbond_it4.39631049
X-RAY DIFFRACTIONr_scangle_it6.1434.5982
X-RAY DIFFRACTIONr_rigid_bond_restr2.63122797
X-RAY DIFFRACTIONr_sphericity_free6.22122
X-RAY DIFFRACTIONr_sphericity_bonded5.3622747
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 227
Rwork0.226 4201
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7
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: 0.284 / Rfactor Rwork: 0.226

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