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- PDB-1ka0: The PAPase Hal2p complexed with a sodium ion and the reaction pro... -

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Basic information

Entry
Database: PDB / ID: 1ka0
TitleThe PAPase Hal2p complexed with a sodium ion and the reaction product AMP
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 / 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 MONOPHOSPHATE / 3'(2'),5'-bisphosphate nucleotidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPatel, S. / Albert, A. / Blundell, T.L.
CitationJournal: To be Published
Title: Hal2p: Ion selectivity and implications on inhibition mechanism
Authors: Patel, S. / Albert, A. / Blundell, T.L.
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 / software / 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_alt_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_alt_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 / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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: Halotolerance protein HAL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5693
Polymers39,1991
Non-polymers3702
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.600, 45.110, 71.600
Angle α, β, γ (deg.)90.00, 111.36, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
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 sodium 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 0.5 M sodium chloride for 1 hour.) , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 5, 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: 1.8→24 Å / Num. all: 26475 / Num. obs: 26475 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.7
Reflection shellResolution: 1.8→1.846 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1829 / % possible all: 87.5

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Processing

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

1qgx


Resolution: 1.8→24 Å / SU B: 3.84 / SU ML: 0.12 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19539 1591 6 %RANDOM
Rwork0.1466 ---
all0.14951 26475 --
obs0.14951 26475 87.21 %-
Displacement parametersBiso mean: 15.345 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.28 Å2
2--0.41 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 24 274 3027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_mcbond_it1.738
X-RAY DIFFRACTIONp_mcangle_it2.557
X-RAY DIFFRACTIONp_scbond_it3.783
X-RAY DIFFRACTIONp_scangle_it5.574
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 119 -
Rwork0.249 --
obs-1829 87.5 %

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