[English] 日本語
Yorodumi
- PDB-4xti: Structure of IMP dehydrogenase of Ashbya gossypii with IMP bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xti
TitleStructure of IMP dehydrogenase of Ashbya gossypii with IMP bound to the active site
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMP dehydrogenase / IMP
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase/GMP reductase / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase/GMP reductase / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / : / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesAshbya gossypii ATCC 10895 (unknown)
Ashbya gossypii (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBuey, R.M. / Ledesma-Amaro, R. / Balsera, M. / de Pereda, J.M. / Revuelta, J.L.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Increased riboflavin production by manipulation of inosine 5'-monophosphate dehydrogenase in Ashbya gossypii.
Authors: Buey, R.M. / Ledesma-Amaro, R. / Balsera, M. / de Pereda, J.M. / Revuelta, J.L.
History
DepositionJan 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8326
Polymers89,0572
Non-polymers7754
Water7,476415
1
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,66312
Polymers178,1144
Non-polymers1,5498
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-x+1,-y+3,z1
crystal symmetry operation3_765-y+2,x+1,z1
crystal symmetry operation4_475y-1,-x+2,z1
Buried area23330 Å2
ΔGint-146 kcal/mol
Surface area47190 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,66312
Polymers178,1144
Non-polymers1,5498
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area23390 Å2
ΔGint-145 kcal/mol
Surface area47600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.775, 117.775, 56.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

-
Components

#1: Protein Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase / IMPDH / IMP dehydrogenase / IMPDH / IMP dehydrogenase / IMPDH


Mass: 44528.555 Da / Num. of mol.: 2 / Fragment: UNP residues 11-119,UNP residues 236-522
Mutation: The whole CBS domain (residuoes 120-235) has been replaced by the sequence stretch SQDG. All residues numbered according to the full-length wild type protein.
Source method: isolated from a genetically manipulated source
Details: IMP bound to the active site
Source: (gene. exp.) Ashbya gossypii ATCC 10895 (unknown), (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (unknown)
Gene: AGOS_AER117W / Production host: Escherichia coli (E. coli) / References: UniProt: Q756Z6, IMP dehydrogenase
#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% (v/v) 1,2 propanediol, 0.1 M phosphate-citrate pH 4.2, 5% (w/v) PEG-3000, 10% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.5→46.88 Å / Num. obs: 124507 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.0898 / Net I/σ(I): 15.15
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 11.75 % / Rmerge(I) obs: 1.467 / Mean I/σ(I) obs: 1.43 / CC1/2: 0.655 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AVF
Resolution: 1.5→46.884 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.03 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1778 6129 4.92 %
Rwork0.1558 --
obs0.1614 124497 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→46.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5425 0 48 415 5888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035569
X-RAY DIFFRACTIONf_angle_d0.6417547
X-RAY DIFFRACTIONf_dihedral_angle_d10.5481923
X-RAY DIFFRACTIONf_chiral_restr0.023892
X-RAY DIFFRACTIONf_plane_restr0.003960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5004-1.52620.31513230.29685842X-RAY DIFFRACTION95
1.5262-1.5540.28543080.26755859X-RAY DIFFRACTION95
1.554-1.58390.26023330.26155851X-RAY DIFFRACTION95
1.5839-1.61620.2662820.25345961X-RAY DIFFRACTION95
1.6162-1.65130.23052870.23055873X-RAY DIFFRACTION95
1.6513-1.68970.21322830.22445884X-RAY DIFFRACTION95
1.6897-1.7320.23233020.21995892X-RAY DIFFRACTION95
1.732-1.77880.20473000.20385909X-RAY DIFFRACTION95
1.7788-1.83110.2232910.25929X-RAY DIFFRACTION95
1.8311-1.89020.22082790.20295911X-RAY DIFFRACTION95
1.8902-1.95780.18572940.19765907X-RAY DIFFRACTION95
1.9578-2.03610.20583230.18815887X-RAY DIFFRACTION95
2.0361-2.12880.20043220.18145851X-RAY DIFFRACTION95
2.1288-2.2410.17033340.17375891X-RAY DIFFRACTION95
2.241-2.38130.17523370.16585901X-RAY DIFFRACTION95
2.3813-2.56510.17853390.15775901X-RAY DIFFRACTION95
2.5651-2.8230.15212730.15295966X-RAY DIFFRACTION96
2.823-3.2310.18142680.14575979X-RAY DIFFRACTION96
3.231-4.06880.15373020.12526007X-RAY DIFFRACTION95
4.0688-28.31240.1673490.12746074X-RAY DIFFRACTION95
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.34390.2144-0.1010.21040.04740.1969-0.1299-0.2180.11270.34560.0934-0.0628-0.06040.03970.00010.28940.0169-0.01990.2783-0.01060.171957.3587154.9576-13.1981
20.52620.02260.08630.47820.04690.3463-0.01790.0864-0.0582-0.08510.02430.0653-0.0216-0.045300.1878-0.0097-0.00380.201-0.00150.159929.489160.4133-35.3336
30.22860.09530.03210.0713-0.09030.3442-0.04560.05030.0191-0.04520.04470.16910.0044-0.09610.00010.2203-0.0063-0.03060.2485-0.00270.245315.6429164.5315-36.1551
40.05520.0147-0.00280.03520.06320.1320.02220.04470.03220.0027-0.04810.2385-0.0163-0.1448-00.20120.01480.00120.2242-0.01030.23318.755174.873-27.7206
50.6726-0.25060.07040.84310.13820.5165-0.0064-0.0456-0.02350.02810.00440.0308-0.0320.015600.1776-0.0037-0.00290.16850.00130.146633.2693170.6144-26.0979
60.18840.1897-0.05080.1913-0.06060.2584-0.03980.22440.0069-0.1727-0.0018-0.0001-0.0347-0.011300.2749-0.0209-0.01230.3030.00180.212634.3628172.0526-49.0121
70.29120.0637-0.06290.18520.00020.07010.006-0.06640.01170.02320.00460.0388-0.0768-0.0078-00.20680.0028-0.00470.2051-0.00320.164340.2903152.66-28.9041
80.183-0.0446-0.02250.13440.08330.05170.08550.11920.0713-0.0591-0.00560.0288-0.0747-0.1363-00.24170.0146-0.0120.25220.02610.233155.7135161.7462-34.4113
90.9005-0.43-0.04060.5545-0.01350.1995-0.01420.03190.10030.02360.0151-0.0706-0.00520.000100.2043-0.0129-0.01680.18690.00080.15297.8016144.2428-16.1975
100.1988-0.2106-0.1210.2947-0.01660.3660.00750.02530.17420.03980.0231-0.0033-0.14620.0074-00.24930.0233-0.0170.2199-0.030.237-8.6154161.8485-9.1246
110.1271-0.0404-0.11450.13020.05730.1069-0.0390.06990.12240.00290.0664-0.0895-0.0658-0.0293-00.20190.0162-0.02350.19190.00230.2046-14.8536155.3155-17.6552
120.9331-0.0031-0.01640.59850.26320.6643-0.01880.00970.0327-0.03480.0103-0.04870.0193-0.042500.17590.0003-0.00410.17130.00090.1401-4.9696143.5972-18.9458
130.09710.0094-0.070.2832-0.04050.1672-0.0558-0.23480.00070.17150.04770.0081-0.014-0.05730.00010.3040.0129-0.00960.2999-0.00040.2089-5.6288142.33813.9173
140.0522-0.04560.02650.0411-0.01780.037-0.0519-0.16210.00640.14410.0615-0.03530.05120.132-00.2310.0003-0.01660.2266-0.01880.224414.7738144.7154-9.4414
150.3879-0.20570.08270.40430.16670.1676-0.0162-0.0742-0.01710.06110.00050.01440.02280.00230.00010.2231-0.0095-0.00760.24350.00030.223412.6608132.8296-15.6836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 268 )
4X-RAY DIFFRACTION4chain 'A' and (resid 269 through 296 )
5X-RAY DIFFRACTION5chain 'A' and (resid 297 through 389 )
6X-RAY DIFFRACTION6chain 'A' and (resid 390 through 459 )
7X-RAY DIFFRACTION7chain 'A' and (resid 460 through 492 )
8X-RAY DIFFRACTION8chain 'A' and (resid 493 through 521 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 114 )
10X-RAY DIFFRACTION10chain 'B' and (resid 115 through 268 )
11X-RAY DIFFRACTION11chain 'B' and (resid 269 through 296 )
12X-RAY DIFFRACTION12chain 'B' and (resid 297 through 389 )
13X-RAY DIFFRACTION13chain 'B' and (resid 390 through 459 )
14X-RAY DIFFRACTION14chain 'B' and (resid 460 through 478 )
15X-RAY DIFFRACTION15chain 'B' and (resid 479 through 521 )

+
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