[English] 日本語
Yorodumi
- PDB-1ka1: The PAPase Hal2p complexed with calcium and magnesium ions and re... -

+
Open data


ID or keywords:

Loading...

-
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 / 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-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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more