[English] 日本語
Yorodumi
- PDB-3t0j: Crystal structure of inositol monophosphatase - II from Staphyloc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t0j
TitleCrystal structure of inositol monophosphatase - II from Staphylococcus aureus MSSA476
ComponentsInositol monophosphatase family protein
KeywordsHYDROLASE / FIG superfamily / Phosphatase
Function / homologyD-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 / PHOSPHATE ION / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsDutta, A. / Bhattacharyya, S. / Dutta, D. / Das, A.K.
CitationJournal: to be published
Title: Crystal structure of inositol monophosphatase - II from Staphylococcus aureus MSSA476
Authors: Dutta, A. / Bhattacharyya, S. / Dutta, D. / Das, A.K.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Inositol monophosphatase family protein
B: Inositol monophosphatase family protein
C: Inositol monophosphatase family protein
D: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,38614
Polymers125,8414
Non-polymers1,54510
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-11 kcal/mol
Surface area41670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.137, 55.209, 149.470
Angle α, β, γ (deg.)90.000, 124.330, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Inositol monophosphatase family protein / IMPase II


Mass: 31460.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MSSA476 / Gene: SAS1042 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q6GAA7
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.43 Å3/Da / Density % sol: 49.28 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.3M Ammonium dihydrogen phosphate, 25% (w/v) PEG 3350, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.586→123.436 Å / Num. all: 37905 / Num. obs: 37905 / % possible obs: 99 % / Redundancy: 6.3 % / Rsym value: 0.163 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.59-2.7360.6870.6271.23150252750.2760.6870.627395.1
2.73-2.896.30.5420.4961.63310152580.2150.5420.4963.8100
2.89-3.096.30.3780.3472.23111849310.150.3780.3475.2100
3.09-3.346.30.2730.253.12902045960.1090.2730.257100
3.34-3.666.40.1680.1544.62684242260.0670.1680.15410.4100
3.66-4.096.30.1240.1146.62446338540.0490.1240.11413.6100
4.09-4.726.30.0980.0898.22162334090.0390.0980.08916.6100
4.72-5.786.30.0980.08981836028960.0390.0980.08916.2100
5.78-8.186.30.0990.097.91427922720.040.0990.0915.4100
8.18-19.7376.10.0530.04812.1720011880.0220.0530.04825.192.7

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→19.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.871 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.611 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 1899 5 %RANDOM
Rwork0.1831 ---
obs0.1874 37905 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.19 Å2 / Biso mean: 30.198 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å2-1.83 Å2
2--2.9 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.59→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8097 0 92 294 8483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228375
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9611372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17251045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45825.414399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.244151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0591530
X-RAY DIFFRACTIONr_chiral_restr0.1220.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216414
X-RAY DIFFRACTIONr_mcbond_it0.6151.55189
X-RAY DIFFRACTIONr_mcangle_it1.1528340
X-RAY DIFFRACTIONr_scbond_it1.84733186
X-RAY DIFFRACTIONr_scangle_it3.0344.53030
LS refinement shellResolution: 2.586→2.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 127 -
Rwork0.242 2441 -
all-2568 -
obs--90.17 %
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)
12.104-0.53210.2931.0968-0.30941.05640.011-0.1222-0.06890.0858-0.0255-0.03240.0625-0.08680.01450.1359-0.01690.00180.01810.0010.0906-11.8626-28.073154.18
21.06450.1110.54710.90630.5113.04170.07720.1617-0.0334-0.0571-0.0258-0.08590.10340.1852-0.05140.02390.02070.0180.0330.00360.062.1643-19.756228.2414
32.3828-0.01730.07050.74430.43861.65740.02820.22580.05410.0235-0.0490.01010.0319-0.05730.02080.0169-0.0014-0.00140.07280.01310.0035-31.3013-19.41768.0582
41.30260.0379-0.08321.2141-0.72852.55870.01120.0465-0.03470.0850.03670.142-0.149-0.3972-0.04790.01920.03120.01920.1018-0.00040.0393-47.4467-11.831333.5633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 272
2X-RAY DIFFRACTION2B0 - 265
3X-RAY DIFFRACTION3C0 - 271
4X-RAY DIFFRACTION4D1 - 265

+
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