[English] 日本語
Yorodumi
- PDB-5uuv: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uuv
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with a product IMP and the inhibitor P182
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
IMP dehydrogenase / GMP reductase 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase 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 / 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
Chem-8L1 / INOSINIC ACID / : / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKim, Y. / Maltseva, N. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 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 a product IMP and the inhibitor P182
Authors: Kim, Y. / Maltseva, N. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,55918
Polymers162,8384
Non-polymers3,72114
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24980 Å2
ΔGint-138 kcal/mol
Surface area47350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.281, 89.164, 164.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 40709.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: internal deletion, residues 92-220 are replaced with GLY-GLY
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: guaB, GBAA_0008, A8C77_00065, ABW01_29210 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic
References: UniProt: Q81W29, UniProt: A0A6L8P2U9*PLUS, IMP dehydrogenase

-
Non-polymers , 5 types, 54 molecules

#2: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-8L1 / N-{4-chloro-3-[4-(trifluoromethyl)-1,3-thiazol-2-yl]phenyl}-N'-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea


Mass: 496.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H20ClF3N4O2S
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.25 M ammonium sulfate, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 32718 / % possible obs: 95.9 % / Redundancy: 5 % / Rsym value: 0.143 / Net I/σ(I): 11.8
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.02 / Num. unique obs: 1610 / CC1/2: 0.684 / Rsym value: 0.794 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJM

4mjm


Resolution: 2.75→46.666 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1669 5.11 %ramdom
Rwork0.1941 ---
obs0.1965 32660 94.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.2 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10169 0 240 40 10449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310577
X-RAY DIFFRACTIONf_angle_d0.88414333
X-RAY DIFFRACTIONf_dihedral_angle_d20.4163840
X-RAY DIFFRACTIONf_chiral_restr0.0471665
X-RAY DIFFRACTIONf_plane_restr0.0031832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7132-2.79310.29461140.25172056X-RAY DIFFRACTION76
2.7931-2.88320.29451630.2512580X-RAY DIFFRACTION97
2.8832-2.98620.28491490.25272598X-RAY DIFFRACTION97
2.9862-3.10580.31671370.24942623X-RAY DIFFRACTION97
3.1058-3.24710.29221460.23472632X-RAY DIFFRACTION97
3.2471-3.41820.28721460.22642633X-RAY DIFFRACTION96
3.4182-3.63230.28421550.21922600X-RAY DIFFRACTION97
3.6323-3.91260.22021280.18962625X-RAY DIFFRACTION96
3.9126-4.30610.21941250.16972651X-RAY DIFFRACTION96
4.3061-4.92860.21081460.15012627X-RAY DIFFRACTION95
4.9286-6.20730.21231330.1752649X-RAY DIFFRACTION95
6.2073-46.67290.20461270.17512717X-RAY DIFFRACTION92
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)
11.609-0.0299-0.69431.51870.16231.39930.01880.2883-0.0918-0.131-0.1368-0.0436-0.1259-0.15560.06780.450.0094-0.07830.3389-0.09140.327917.79254.463524.9899
22.84440.15710.6810.71670.98392.30330.09360.080.0868-0.0707-0.17430.147-0.0696-0.22820.06390.3512-0.0163-0.00310.3367-0.06660.34596.65862.286325.4164
33.9282-1.3532-1.54842.9341-0.14981.32810.2760.02060.56290.2015-0.06340.0633-0.274-0.1101-0.23920.4203-0.0528-0.01210.478-0.02040.390617.413617.704428.7568
44.37451.23973.09264.17774.10237.4789-0.0928-0.38480.3061-0.20820.0024-0.1264-0.2582-0.40360.17280.31470.04490.05020.41310.06750.405433.11776.155830.9869
522.00021.99991.9999222.729812.3683-2.0649-8.3621-0.4343-5.0954.220112.7074-2.32461.02820.10160.4721.0831-0.53720.991128.913419.986533.3342
63.385-0.2324-3.7182.02420.79967.31160.26860.27660.0509-0.113-0.1166-0.063-0.1726-0.2936-0.08680.2632-0.0288-0.07360.40560.03380.373235.3407-6.336864.9572
74.69111.35690.1935.0356-1.12564.73190.0812-0.2247-0.1783-0.19140.0243-0.00280.0918-0.0663-0.1180.2496-0.0058-0.03830.3933-0.03840.282948.26437.989581.5984
88.0763-1.278-2.19293.24481.07567.0437-0.1569-0.6962-0.10470.06980.216-0.4506-0.21161.0763-0.06010.3354-0.0094-0.03080.5942-0.03740.54260.42029.101883.9109
90.91130.3958-1.12993.16274.18188.73820.1933-0.00160.3289-0.3612-0.10140.0105-0.07480.6801-0.24120.34020.0856-0.0370.57240.04520.550961.2395-1.806373.7105
102.02720.23670.16051.19640.43643.509-0.0665-0.1082-0.0680.11150.0913-0.13020.37160.0577-0.01380.3210.0107-0.00580.3268-0.01190.355247.431-2.8968.4962
112.90860.9008-0.11082.74650.13664.3727-0.07070.10160.7891-0.412-0.0038-0.6307-0.9648-0.25020.02140.51490.0538-0.00720.3737-0.02360.491944.864318.381571.2364
123.41292.25860.15042.72840.07921.15880.0331-0.34850.05850.106-0.24340.1992-0.249-0.06960.24050.37060.1051-0.04270.5798-0.08170.313238.310611.742173.53
133.3071-2.01070.54242.999-0.93493.23450.1056-0.09890.3024-0.1995-0.0664-0.2723-0.0637-0.192-0.11390.3066-0.1223-0.00970.5998-0.04370.552826.93332.81868.0149
141.31020.336-0.68791.9632-0.94881.3973-0.05790.18890.0589-0.0595-0.0382-0.26220.02560.1660.10990.33370.09510.0610.50290.00450.454554.81245.582237.3924
153.173-0.0169-0.35852.0874-0.75481.44560.04370.5344-0.0331-0.3738-0.1814-0.24640.06880.13010.10850.51270.07870.07480.45410.00340.393655.06826.29321.9234
163.1263-0.18620.36933.3606-1.09252.2346-0.0126-0.03230.035-0.18840.0478-0.2021-0.07260.14970.00730.3370.00870.00980.294-0.05540.316952.38664.616237.5319
172.8717-0.22891.94671.5576-0.62372.8484-0.331-0.19140.63590.05560.01660.0777-0.63340.04420.28660.35740.0267-0.00870.348-0.09550.45549.634219.649838.0399
183.3463-1.0556-1.77766.59490.83754.00680.0693-0.13280.57710.4781-0.0592-0.0003-0.0552-0.3381-0.03910.4529-0.0366-0.1220.6305-0.04310.390748.61825.251752.8413
192.8525-0.3577-0.12721.41690.24950.9332-0.13460.0936-0.0908-0.03160.11940.04980.0584-0.2430.04710.3373-0.10850.030.3869-0.00120.35388.4644-2.421258.3986
204.1706-0.1831.51073.4602-1.37323.73250.0411-0.41290.14910.38520.09840.4029-0.1422-0.4148-0.14950.3726-0.00220.05750.6265-0.06530.4272-2.61398.136877.3854
212.7369-0.52210.75222.236-0.60731.9086-0.1272-0.32430.42190.39950.3813-0.20740.09-0.2076-0.01860.3888-0.10280.01520.58350.0080.4115.9857-4.929479.9314
221.65840.4568-0.04840.6663-0.63881.5478-0.054-0.0651-0.203-0.12170.01590.05630.194-0.2704-0.01110.3495-0.0427-0.00650.3915-0.01370.350110.5063-4.016465.6356
233.6628-0.39192.33095.5152-1.15186.8431-0.2154-0.08040.57310.5523-0.1694-0.0365-0.6668-0.29170.34710.46220.0257-0.04550.4852-0.07480.481610.093520.702267.6637
240.81730.23381.19742.71981.85764.79010.11040.0172-0.0586-0.408-0.01120.0523-0.4891-0.21820.060.27320.03120.07830.39060.01440.32647.580311.59660.2475
253.4280.5031-0.78085.49121.00083.29430.4638-0.1680.5074-0.193-0.32940.0353-0.435-0.0969-0.03430.4296-0.0066-0.02710.6993-0.03960.37311.48514.071846.4231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 355 )
3X-RAY DIFFRACTION3chain 'A' and (resid 356 through 446 )
4X-RAY DIFFRACTION4chain 'A' and (resid 447 through 485 )
5X-RAY DIFFRACTION5chain 'A' and (resid 486 through 486 )
6X-RAY DIFFRACTION6chain 'B' and (resid -1 through 33 )
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 77 )
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 242 )
9X-RAY DIFFRACTION9chain 'B' and (resid 243 through 270 )
10X-RAY DIFFRACTION10chain 'B' and (resid 271 through 356 )
11X-RAY DIFFRACTION11chain 'B' and (resid 357 through 398 )
12X-RAY DIFFRACTION12chain 'B' and (resid 399 through 446 )
13X-RAY DIFFRACTION13chain 'B' and (resid 447 through 485 )
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 77 )
15X-RAY DIFFRACTION15chain 'C' and (resid 78 through 319 )
16X-RAY DIFFRACTION16chain 'C' and (resid 320 through 376 )
17X-RAY DIFFRACTION17chain 'C' and (resid 377 through 446 )
18X-RAY DIFFRACTION18chain 'C' and (resid 447 through 485 )
19X-RAY DIFFRACTION19chain 'D' and (resid -1 through 56 )
20X-RAY DIFFRACTION20chain 'D' and (resid 57 through 242 )
21X-RAY DIFFRACTION21chain 'D' and (resid 243 through 270 )
22X-RAY DIFFRACTION22chain 'D' and (resid 271 through 363 )
23X-RAY DIFFRACTION23chain 'D' and (resid 364 through 398 )
24X-RAY DIFFRACTION24chain 'D' and (resid 399 through 446 )
25X-RAY DIFFRACTION25chain 'D' and (resid 447 through 485 )

+
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