[English] 日本語
Yorodumi
- PDB-5d92: Structure of a phosphatidylinositolphosphate (PIP) synthase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d92
TitleStructure of a phosphatidylinositolphosphate (PIP) synthase from Renibacterium Salmoninarum
ComponentsAF2299 protein,Phosphatidylinositol synthase
KeywordsMEMBRANE PROTEIN / Enzyme / lipid biosynthesis / phosphatidylinositol
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phosphotransferase activity, for other substituted phosphate groups / phospholipid biosynthetic process / nucleotide binding / magnesium ion binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A - #30 / Phosphatidylinositol phosphate synthase PgsA1 / : / CDP-alcohol phosphatidyltransferase AF_2299-like, N-terminal / CDP-alcohol phosphotransferase transmembrane (TM) domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. ...Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A - #30 / Phosphatidylinositol phosphate synthase PgsA1 / : / CDP-alcohol phosphatidyltransferase AF_2299-like, N-terminal / CDP-alcohol phosphotransferase transmembrane (TM) domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-58A / Octadecane / Phosphatidylinositol phosphate synthase / CDP-alcohol phosphatidyltransferase AF-2299-like N-terminal domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Renibacterium salmoninarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å
AuthorsClarke, O.B. / Tomasek, D.T. / Jorge, C.D. / Belcher Dufrisne, M. / Kim, M. / Banerjee, S. / Rajashankar, K.R. / Hendrickson, W.A. / Santos, H. / Mancia, F.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for phosphatidylinositol-phosphate biosynthesis.
Authors: Clarke, O.B. / Tomasek, D. / Jorge, C.D. / Dufrisne, M.B. / Kim, M. / Banerjee, S. / Rajashankar, K.R. / Shapiro, L. / Hendrickson, W.A. / Santos, H. / Mancia, F.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: AF2299 protein,Phosphatidylinositol synthase
A: AF2299 protein,Phosphatidylinositol synthase
B: AF2299 protein,Phosphatidylinositol synthase
C: AF2299 protein,Phosphatidylinositol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,00949
Polymers150,3914
Non-polymers12,61745
Water00
1
D: AF2299 protein,Phosphatidylinositol synthase
A: AF2299 protein,Phosphatidylinositol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,39528
Polymers75,1962
Non-polymers7,19926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-63 kcal/mol
Surface area33050 Å2
MethodPISA
2
B: AF2299 protein,Phosphatidylinositol synthase
C: AF2299 protein,Phosphatidylinositol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,61421
Polymers75,1962
Non-polymers5,41819
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-62 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.002, 62.489, 169.759
Angle α, β, γ (deg.)90.000, 99.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: -137 - 204 / Label seq-ID: 1 - 342

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAB
2chain BBC
3chain CCD
4chain DDA

-
Components

#1: Protein
AF2299 protein,Phosphatidylinositol synthase


Mass: 37597.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea), (gene. exp.) Renibacterium salmoninarum (bacteria)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126, ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
Gene: AF_2299, RSal33209_2010 / Production host: Escherichia coli (E. coli) / References: UniProt: O27985, UniProt: A9WSF5
#2: Chemical...
ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C18H38
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-58A / 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine / cytidinediphosphate-dioleoylglycerol / CDP-1,2-dioleoyl-sn-glycerol


Mass: 1006.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C48H85N3O15P2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30% (v/v) PEG 300, 0.1 M MES pH 6.0, 0.1 M sodium chloride, 0.1 M magnesium chloride (precipitant); Concentrated protein was mixed with molten monoolein in a 1:1.5 (w/w) ratio of protein: ...Details: 30% (v/v) PEG 300, 0.1 M MES pH 6.0, 0.1 M sodium chloride, 0.1 M magnesium chloride (precipitant); Concentrated protein was mixed with molten monoolein in a 1:1.5 (w/w) ratio of protein:lipid using coupled syringes. A Mosquito LCP (TTP Labtech) robot was used to dispense a typical volume of 50-75 nL of protein/lipid mixture onto a 96-well glass sandwich plate, which was covered with 750 nL precipitant solution. Monoolein was doped with 2% CDP-DAG.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.62→166.97 Å / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 79.39 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.15 / Net I/σ(I): 5 / Num. measured all: 78622
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.62-3.973.80.931.41836748780.6160.55297.9
8.87-166.973.60.04219.3544715030.9980.02698.8

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D91

5d91


Resolution: 3.62→166.97 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2997 1043 4.92 %Random selection
Rwork0.2801 20175 --
obs0.2811 21218 98.41 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.71 Å2 / Biso mean: 76.5321 Å2 / Biso min: 26.35 Å2
Refinement stepCycle: final / Resolution: 3.62→166.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10350 0 495 0 10845
Biso mean--63.13 --
Num. residues----1358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01611061
X-RAY DIFFRACTIONf_angle_d1.06814869
X-RAY DIFFRACTIONf_chiral_restr0.0411776
X-RAY DIFFRACTIONf_plane_restr0.0051785
X-RAY DIFFRACTIONf_dihedral_angle_d12.1883944
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6080X-RAY DIFFRACTION8.517TORSIONAL
12B6080X-RAY DIFFRACTION8.517TORSIONAL
13C6080X-RAY DIFFRACTION8.517TORSIONAL
14D6080X-RAY DIFFRACTION8.517TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.613-3.80360.42211690.37642709287895
3.8036-4.04190.29841480.32652888303699
4.0419-4.3540.30971540.29942854300899
4.354-4.79220.3031190.292829363055100
4.7922-5.48560.32331420.2762889303199
5.4856-6.91140.31131520.2922922307499
6.9114-167.47650.22091590.2072977313698

+
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