[English] 日本語
Yorodumi
- PDB-2ofx: crystal structure of the APSK domain of human PAPSS1 in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ofx
Titlecrystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS
ComponentsBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1
KeywordsTRANSFERASE / nucleotide kinase
Function / homology
Function and homology information


3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and synthesis of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / nucleotidyltransferase activity / skeletal system development ...3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and synthesis of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / nucleotidyltransferase activity / skeletal system development / Signaling by BRAF and RAF1 fusions / phosphorylation / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate kinase / PUA-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases ...Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate kinase / PUA-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSekulic, N. / Lavie, A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Elucidation of the Active Conformation of the APS-Kinase Domain of Human PAPS Synthetase 1.
Authors: Sekulic, N. / Dietrich, K. / Paarmann, I. / Ort, S. / Konrad, M. / Lavie, A.
History
DepositionJan 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_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.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_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_ref_seq_dif.details / _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: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1
B: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,15512
Polymers45,8582
Non-polymers2,29710
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-101 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 63.320, 61.690
Angle α, β, γ (deg.)90.000, 114.380, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1


Mass: 22928.861 Da / Num. of mol.: 2 / Fragment: APS kinase domain (Residues 1-227)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS1 / Plasmid: pGEX-RB with engineered TEV cutting site / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Codon Plus / References: UniProt: O43252, adenylyl-sulfate kinase

-
Non-polymers , 5 types, 207 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PPS / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE


Mass: 507.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O13P2S
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: reservoir: 0.2-0.4mM ammonium dihydrogenphosphate protein solution: 6 mg/ml protein, 2 mM PAPS, 2 mM ADP, 5 mM MgCl2, 50 mM Tris pH 7.5, 50 mM KCl , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→20 Å / Num. all: 28560 / Num. obs: 27832 / % possible obs: 97.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.079 / Rsym value: 0.071 / Net I/σ(I): 18.83
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 5.13 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 9.3 / Num. unique all: 4298 / Rsym value: 0.148 / % possible all: 94.5

-
Phasing

Phasing MRRfactor: 0.464 / Cor.coef. Fo:Fc: 0.309
Highest resolutionLowest resolution
Rotation3 Å28.25 Å
Translation3 Å28.25 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OFW

2ofw


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.888 / SU B: 3.763 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2766 10 %RANDOM
Rwork0.187 ---
obs0.192 27683 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20.11 Å2
2--1.16 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 176 197 3546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213415
X-RAY DIFFRACTIONr_angle_refined_deg1.5712.0164666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38124.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63715534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.151526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022564
X-RAY DIFFRACTIONr_nbd_refined0.210.21966
X-RAY DIFFRACTIONr_nbtor_refined0.310.22309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2342
X-RAY DIFFRACTIONr_metal_ion_refined0.0450.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.212
X-RAY DIFFRACTIONr_mcbond_it0.7731.52073
X-RAY DIFFRACTIONr_mcangle_it1.2623266
X-RAY DIFFRACTIONr_scbond_it2.02131520
X-RAY DIFFRACTIONr_scangle_it2.9674.51400
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 184 -
Rwork0.209 1669 -
obs-1853 89.91 %

+
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://pdbjlvh1.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