[English] 日本語
Yorodumi
- PDB-3qw2: L-myo-inositol 1-phosphate synthase from Archaeoglobus mutant N255A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qw2
TitleL-myo-inositol 1-phosphate synthase from Archaeoglobus mutant N255A
ComponentsMyo-inositol-1-phosphate synthase (Ino1)
KeywordsISOMERASE / L-myo-inositol 1-phosphate synthase
Function / homology
Function and homology information


inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / nucleotide binding / membrane
Similarity search - Function
Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase, GAPDH-like / Myo-inositol-1-phosphate synthase / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase, GAPDH-like / Myo-inositol-1-phosphate synthase / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Myo-inositol-1-phosphate synthase (Ino1)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsNeelon, K. / Roberts, M.F. / Stec, B.
CitationJournal: Biophys.J. / Year: 2011
Title: Crystal structure of a trapped catalytic intermediate suggests that forced atomic proximity drives the catalysis of mIPS.
Authors: Neelon, K. / Roberts, M.F. / Stec, B.
History
DepositionFeb 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Dec 7, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _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_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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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
A: Myo-inositol-1-phosphate synthase (Ino1)
B: Myo-inositol-1-phosphate synthase (Ino1)
C: Myo-inositol-1-phosphate synthase (Ino1)
D: Myo-inositol-1-phosphate synthase (Ino1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,00025
Polymers174,8974
Non-polymers4,10421
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23370 Å2
ΔGint-290 kcal/mol
Surface area48560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.512, 88.036, 103.727
Angle α, β, γ (deg.)90.00, 94.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 392 / Label seq-ID: 1 - 392

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Myo-inositol-1-phosphate synthase (Ino1) / mIPS


Mass: 43724.133 Da / Num. of mol.: 4 / Mutation: N255A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF1794, AF_1794 / Production host: Escherichia coli (E. coli) / References: UniProt: O28480, inositol-3-phosphate synthase

-
Non-polymers , 6 types, 507 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M calcium chloride, 14% PEG400, 15% PEG1500, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 11, 2005 / Details: Osmic Blue
RadiationMonochromator: Osmic Blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→103.14 Å / Num. all: 49303 / Num. obs: 46724 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 8.5
Reflection shellResolution: 2.59→2.64 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.2 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
CrystalCleardata collection
CrystalCleardata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1I

1u1i


Resolution: 2.59→103.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.862 / SU B: 29.863 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26735 2506 5.1 %RANDOM
Rwork0.18466 ---
obs0.18896 46724 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.609 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å2-0.12 Å2
2---1.31 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.59→103.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12324 0 251 486 13061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.99217394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53451564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51324.328536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.235152232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9671548
X-RAY DIFFRACTIONr_chiral_restr0.1070.21888
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219508
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.27286
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.28725
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2768
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2170.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5941.57776
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.091212464
X-RAY DIFFRACTIONr_scbond_it1.45835082
X-RAY DIFFRACTIONr_scangle_it2.3654.54930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3081 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.440.5
Bmedium positional0.410.5
Cmedium positional0.430.5
Dmedium positional0.520.5
Amedium thermal0.632
Bmedium thermal0.632
Cmedium thermal0.642
Dmedium thermal0.672
LS refinement shellResolution: 2.593→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 182 -
Rwork0.292 3362 -
obs--94.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.32010.5048-0.23091.4888-0.3271.31710.1408-0.17680.02430.2953-0.08150.0089-0.0884-0.0842-0.05930.15950.0090.09990.15880.0060.10160.058614.307750.4452
21.36390.48290.4921.0714-0.11470.28460.1481-0.2255-0.03510.2044-0.09120.12320.0059-0.1234-0.05690.1433-0.00730.00380.17910.00650.161410.228-4.041932.0981
31.11770.69590.90241.3090.55472.1366-0.0554-0.08350.01510.03460.12040.0878-0.0182-0.2208-0.0650.0870.03860.070.17820.0340.1782-7.67249.893634.8005
41.206-0.2954-0.09541.4739-0.35751.4160.12470.317-0.0362-0.4125-0.08230.02690.1081-0.1136-0.04230.1890.023-0.06730.2014-0.04320.09323.0585-9.4342-6.904
50.58330.0465-0.15121.0670.02040.59470.0930.0945-0.028-0.2104-0.09340.0592-0.092-0.11130.00040.13180.03280.00380.1461-0.0110.132113.13756.404413.4057
61.0914-0.38520.80751.85790.89641.70830.07970.0264-0.0779-0.0513-0.07590.21880.0267-0.3191-0.00380.06850.0173-0.0420.29180.03040.201-6.4362-3.6047.0357
70.77970.22780.39420.9927-0.13351.94110.0789-0.0277-0.08090.0716-0.0054-0.02620.2258-0.0147-0.07350.11310.0336-0.03890.0181-0.01540.10836.9555-31.476933.6784
81.0698-0.12640.36610.4622-0.03350.47180.1272-0.1401-0.10410.2315-0.0024-0.0730.0785-0.0066-0.12480.1844-0.0182-0.02220.10360.02390.11429.3249-5.010834.5437
92.0888-0.28850.64041.8773-0.42910.58660.0968-0.0117-0.08420.041-0.0622-0.2313-0.01690.1081-0.03460.06960.0089-0.02650.133-0.01370.155947.4821-17.67529.4125
100.90510.0849-0.33860.8881-0.79912.40340.0442-0.00780.02180.1385-0.0962-0.138-0.21660.01920.05190.0959-0.043-0.00350.02920.00060.088544.566528.326318.0516
111.1128-0.6572-0.22840.5490.41130.73850.15160.11230.1822-0.1834-0.0554-0.199-0.15710.0209-0.09620.17990.01320.04870.09290.01410.148231.92443.452314.724
121.11740.0746-0.90630.90360.00920.8193-0.0496-0.0492-0.04040.0256-0.0609-0.2150.05570.10390.11050.0875-0.0096-0.00450.10980.05350.204151.079812.440523.5208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 227
2X-RAY DIFFRACTION2A228 - 330
3X-RAY DIFFRACTION3A331 - 392
4X-RAY DIFFRACTION4B1 - 227
5X-RAY DIFFRACTION5B228 - 330
6X-RAY DIFFRACTION6B331 - 392
7X-RAY DIFFRACTION7C1 - 227
8X-RAY DIFFRACTION8C228 - 330
9X-RAY DIFFRACTION9C331 - 392
10X-RAY DIFFRACTION10D1 - 227
11X-RAY DIFFRACTION11D228 - 330
12X-RAY DIFFRACTION12D331 - 392

+
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