[English] 日本語
Yorodumi
- PDB-6mgu: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mgu
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus Anthracis in the complex with inhibitor Oxanosine monophosphate
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IMPDH / TIM barrel / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / 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
Chem-JQS / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKim, Y. / Maltseva, N. / Yu, R. / Hedstrom, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus Anthracis in the complex with inhibitor Oxanosine monophosphate
Authors: Kim, Y. / Maltseva, N. / Yu, R. / Hedstrom, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,98513
Polymers76,4762
Non-polymers1,50911
Water4,252236
1
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,27128
Polymers152,9524
Non-polymers3,31924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area23740 Å2
ΔGint-63 kcal/mol
Surface area46360 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,67024
Polymers152,9524
Non-polymers2,71920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area22450 Å2
ΔGint-75 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.411, 86.411, 90.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 38237.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium)
Gene: guaB, BA_0008, A9486_01210, ABW01_29210, BVG01_30935, COL95_27530
Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0J1HJU0, UniProt: A0A6L8P2U9*PLUS, IMP dehydrogenase

-
Non-polymers , 6 types, 247 molecules

#2: Chemical ChemComp-JQS / 5-[(Z)-(aminomethylidene)amino]-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid


Mass: 366.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N4O9P
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Magnesium Chloride, 0.1 M MES:NaOH pH 6.5, 30% (v/v) PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 97222 / % possible obs: 98.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.56 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.6
Reflection shellResolution: 1.54→1.57 Å / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 0.7 / Num. unique all: 4080 / CC1/2: 0.4 / % possible all: 82.6

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→43.206 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 20.52
RfactorNum. reflection% reflection
Rfree0.1977 4781 4.93 %
Rwork0.1645 --
obs0.1662 97075 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.2 Å2
Refinement stepCycle: LAST / Resolution: 1.54→43.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 96 236 5424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065362
X-RAY DIFFRACTIONf_angle_d1.0067253
X-RAY DIFFRACTIONf_dihedral_angle_d20.6991982
X-RAY DIFFRACTIONf_chiral_restr0.364846
X-RAY DIFFRACTIONf_plane_restr0.005940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.55750.38271390.32952499X-RAY DIFFRACTION81
1.5575-1.57590.32121130.29412909X-RAY DIFFRACTION92
1.5759-1.59510.30521770.25433010X-RAY DIFFRACTION98
1.5951-1.61530.27981410.23593080X-RAY DIFFRACTION98
1.6153-1.63650.26341550.21993127X-RAY DIFFRACTION99
1.6365-1.6590.23961410.2123042X-RAY DIFFRACTION98
1.659-1.68270.21371640.20423068X-RAY DIFFRACTION99
1.6827-1.70780.25641610.19853068X-RAY DIFFRACTION99
1.7078-1.73450.24281400.19433133X-RAY DIFFRACTION99
1.7345-1.76290.24831870.18673061X-RAY DIFFRACTION99
1.7629-1.79330.22111690.18583086X-RAY DIFFRACTION99
1.7933-1.82590.22831750.17993031X-RAY DIFFRACTION99
1.8259-1.8610.20181330.16713111X-RAY DIFFRACTION99
1.861-1.8990.21331680.15943110X-RAY DIFFRACTION99
1.899-1.94030.19481480.1513095X-RAY DIFFRACTION99
1.9403-1.98540.1791630.15223075X-RAY DIFFRACTION100
1.9854-2.03510.19071620.15883145X-RAY DIFFRACTION100
2.0351-2.09010.19161320.15883142X-RAY DIFFRACTION100
2.0901-2.15160.18721600.15673096X-RAY DIFFRACTION100
2.1516-2.22110.21091380.16043150X-RAY DIFFRACTION99
2.2211-2.30040.19221640.15723090X-RAY DIFFRACTION100
2.3004-2.39250.19091850.15463116X-RAY DIFFRACTION100
2.3925-2.50140.18051540.16313109X-RAY DIFFRACTION100
2.5014-2.63330.18421510.16383143X-RAY DIFFRACTION100
2.6333-2.79820.22242000.17643096X-RAY DIFFRACTION99
2.7982-3.01420.22681590.18223128X-RAY DIFFRACTION100
3.0142-3.31750.21111640.18353148X-RAY DIFFRACTION100
3.3175-3.79730.18091910.16363121X-RAY DIFFRACTION100
3.7973-4.78320.15481680.13443126X-RAY DIFFRACTION99
4.7832-43.22250.20821790.15613179X-RAY DIFFRACTION99

+
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