[English] 日本語
Yorodumi
- PDB-5uwx: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uwx
TitleCrystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P176
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
Keywordsoxidoreductase/oxidoreductase inhibitor / TIM barrel / IMPDH / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / 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-8L7 / ACETIC ACID / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMaltseva, N. / Kim, Y. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D.R. / Hedstrom, L. / Joachimiak, A. / Anderson, W.F. / 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 Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P176
Authors: Maltseva, N. / Kim, Y. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D.R. / Hedstrom, L. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Aug 23, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / diffrn_detector / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation_author.name / _diffrn_detector.detector / _pdbx_struct_assembly_prop.value
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
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
C: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,83320
Polymers153,7654
Non-polymers4,06816
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-80 kcal/mol
Surface area58960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.278, 118.943, 96.992
Angle α, β, γ (deg.)90.00, 102.88, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 38441.266 Da / Num. of mol.: 4
Mutation: CBS domain (residues 89-215) is replaced with SGG residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: guaB_2, guaB, ERS852446_02285, JFP838_13815 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: A0A127ELD1, IMP dehydrogenase

-
Non-polymers , 6 types, 493 molecules

#2: Chemical
ChemComp-8L7 / N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-alpha-D-ribofuranosylamine


Mass: 475.965 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30ClN3O5
#3: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium acetate, 0.1M Bis-Tris pH 6.5, 45% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2016 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→47.5 Å / Num. obs: 118158 / % possible obs: 97.5 % / Redundancy: 5.9 % / Rsym value: 0.096 / Net I/σ(I): 16.34
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.79 / Num. unique obs: 5833 / CC1/2: 0.804 / Rsym value: 0.705 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.5 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.2
RfactorNum. reflection% reflection
Rfree0.197 5793 4.9 %
Rwork0.1625 --
obs0.1642 118136 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10131 0 276 477 10884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810693
X-RAY DIFFRACTIONf_angle_d1.02114481
X-RAY DIFFRACTIONf_dihedral_angle_d22.0133988
X-RAY DIFFRACTIONf_chiral_restr0.0641682
X-RAY DIFFRACTIONf_plane_restr0.0051846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8459-1.86680.31981930.28113455X-RAY DIFFRACTION90
1.8668-1.88880.3191990.27153702X-RAY DIFFRACTION96
1.8888-1.91180.28391810.23853602X-RAY DIFFRACTION94
1.9118-1.9360.26741840.23623727X-RAY DIFFRACTION97
1.936-1.96150.24981740.21073772X-RAY DIFFRACTION97
1.9615-1.98840.22321810.20013755X-RAY DIFFRACTION97
1.9884-2.01680.22762150.19153730X-RAY DIFFRACTION97
2.0168-2.04690.24051910.18813689X-RAY DIFFRACTION97
2.0469-2.07890.23642010.18163749X-RAY DIFFRACTION97
2.0789-2.1130.20951930.1713736X-RAY DIFFRACTION98
2.113-2.14940.2131820.17273788X-RAY DIFFRACTION98
2.1494-2.18850.21911920.16853772X-RAY DIFFRACTION98
2.1885-2.23060.2011830.17153745X-RAY DIFFRACTION98
2.2306-2.27610.20742020.16173688X-RAY DIFFRACTION97
2.2761-2.32560.17751800.15853656X-RAY DIFFRACTION95
2.3256-2.37970.21551910.15933787X-RAY DIFFRACTION98
2.3797-2.43920.19072170.15983764X-RAY DIFFRACTION98
2.4392-2.50520.1982080.15843752X-RAY DIFFRACTION98
2.5052-2.57890.20711900.15773790X-RAY DIFFRACTION98
2.5789-2.66210.22030.15743783X-RAY DIFFRACTION98
2.6621-2.75720.20421970.1683788X-RAY DIFFRACTION98
2.7572-2.86760.19832010.16573753X-RAY DIFFRACTION98
2.8676-2.99810.21531840.17383664X-RAY DIFFRACTION94
2.9981-3.15610.19332010.16783783X-RAY DIFFRACTION99
3.1561-3.35380.22291890.16473842X-RAY DIFFRACTION99
3.3538-3.61270.19062250.15963800X-RAY DIFFRACTION99
3.6127-3.97610.16742000.14793809X-RAY DIFFRACTION99
3.9761-4.5510.16671470.1353759X-RAY DIFFRACTION96
4.551-5.73230.18181970.14943869X-RAY DIFFRACTION99
5.7323-47.52190.17861920.15943834X-RAY DIFFRACTION97
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)
13.5618-0.0453-0.88260.42710.48991.79990.1144-0.26750.08070.1711-0.0971-0.1046-0.31780.0149-0.03520.3538-0.05140.03610.23130.01880.23163.98613.508538.3743
21.13880.1657-0.12871.1343-0.06120.69910.1139-0.1959-0.14460.1638-0.0778-0.3022-0.12810.2372-0.03710.302-0.1074-0.01750.32610.01540.346421.6688-3.451237.4188
32.4445-0.7181-0.81891.52570.44871.33650.12590.2024-0.0471-0.1625-0.0831-0.1845-0.20330.1062-0.05990.3218-0.08330.03440.30780.00680.328916.26760.069721.3775
43.18581.36540.33833.13470.14682.85160.0879-0.00230.1439-0.0269-0.1041-0.0407-0.1017-0.13160.01220.29620.06990.05780.1890.02370.3-2.05045.538426.7911
54.20980.19142.40163.68720.56423.58820.0468-0.4224-0.49030.1342-0.1614-0.1105-0.0982-0.05420.06820.2028-0.04560.01530.24530.08420.2439-1.0475-21.455337.1732
61.11940.0265-0.12632.05960.49562.0461-0.03060.027-0.6449-0.10180.051-0.6530.19230.1981-0.02150.2690.05940.06910.30870.01840.76089.2701-45.961125.5199
76.1022-2.5486-0.12451.18-0.58693.25610.02360.3224-0.9009-0.1262-0.1248-0.24410.6654-0.04230.07610.34370.03740.06080.2789-0.02890.7373-0.878-55.495625.2713
83.8705-4.20930.46374.5623-0.44892.0664-0.00350.0012-0.6409-0.0918-0.0709-0.23760.447-0.03590.06080.2838-0.03340.00740.237-0.00490.611-6.9709-51.249531.2598
91.99030.53540.3361.6738-0.03611.3476-0.05860.0181-0.3688-0.06580.009-0.42960.06660.08720.04960.17240.00960.03220.194-0.0020.3881-0.8558-36.03127.4988
106.4662-1.2022-2.11193.51950.38394.5202-0.24930.6977-0.7669-0.35370.0396-0.03110.3201-0.34190.18310.354-0.03380.1020.3445-0.11590.3403-2.8067-38.152511.7767
112.3835-0.63260.12172.77050.73241.31480.0826-0.1624-0.25060.1178-0.0461-0.47810.00640.1787-0.03650.2127-0.0587-0.02240.29370.07180.40919.4198-24.078434.1538
125.5659-3.2403-2.28683.1752-0.82964.51780.03750.4481-0.606-0.7147-0.09910.2919-0.0796-0.01420.09660.3482-0.04440.0150.3539-0.02760.416312.2001-14.895718.0624
131.29510.27650.01662.29050.3251.18320.0230.0446-0.0575-0.075-0.0484-0.126-0.17230.11970.13330.2172-0.0335-0.00950.2988-0.01480.244622.4255-19.8722-31.2159
142.6370.32650.67321.17180.45342.77390.2438-0.6628-0.22090.4913-0.2585-0.49090.08590.4216-0.03630.3629-0.0534-0.14090.6150.15230.395741.9606-26.6003-9.0723
154.7588-3.46822.39553.3819-1.83281.84510.0191-0.22360.03560.1468-0.0547-0.2926-0.06640.26910.05770.2648-0.1268-0.08160.5770.04410.400347.9706-16.0088-17.849
161.67830.13530.11141.869-0.07460.50070.1075-0.09960.04070.0216-0.0964-0.2932-0.08620.2859-0.02650.1949-0.0403-0.01620.37620.01830.257134.378-18.7301-23.1271
171.38660.6515-0.17752.73040.69911.62550.2152-0.6267-0.01450.7244-0.29640.0234-0.02090.24330.08180.3837-0.1153-0.03280.5330.03870.25525.7981-23.6117-5.9205
184.3782-0.7346-1.26322.674-0.71752.64740.0361-0.1361-0.15790.2191-0.04110.0894-0.099-0.019-0.00740.1972-0.0415-0.0470.2283-0.03640.237914.9421-28.992-21.6246
199.04482.32971.68013.17480.73542.94880.3022-0.00510.28490.097-0.23850.0658-0.2345-0.1408-0.04190.2950.05030.05460.22080.03320.177541.1953-61.819929.4916
202.17-0.0634-0.82412.4852-0.23271.93490.0440.24160.57-0.34020.06110.3039-0.805-0.307-0.06940.81180.26570.05870.43010.18650.536540.5252-37.075915.2923
212.5384-2.45460.70483.6493-2.42562.58860.61630.2480.89040.1546-0.3168-0.2982-0.8198-0.0694-0.1070.93860.14010.15880.37270.12840.627248.6202-26.715621.956
223.4327-3.20210.87824.4472-1.81790.88180.093-0.03730.65470.1031-0.0472-0.0693-0.7135-0.22540.02650.76510.08630.12820.25320.01250.412449.3681-32.206229.8853
233.7093-2.87631.34932.6354-1.1060.5043-0.0993-0.46020.43750.4850.0920.0392-0.8155-0.3541-0.03150.67650.15690.09780.3603-0.00260.424245.7251-37.313734.1809
241.49160.61590.2311.1390.21730.7280.0367-0.04360.15120.07040.03380.1445-0.3826-0.1845-0.0770.42440.12170.06590.28710.05990.288246.7203-50.286327.7594
251.14121.1906-0.2711.3799-1.02584.41170.05550.50020.1147-0.37070.17310.0761-0.5979-0.1968-0.25710.53870.07750.02640.37340.11730.347649.5484-47.80877.2948
268.85081.34155.42872.23041.03973.37870.12550.48510.0566-0.20730.0609-0.1515-0.48140.1046-0.07570.5802-0.01180.12680.42530.09090.294457.6185-45.552311.1967
274.0493.4252-3.94333.5611-2.99143.9871-0.04980.4182-0.0753-0.5634-0.3512-0.1614-0.0009-0.10760.26750.42710.2106-0.02440.49080.12820.37733.2268-54.503813.7618
282.09050.09971.0743.0505-0.00884.1180.08840.33040.2415-0.2387-0.11590.1551-0.2713-0.17480.01370.25770.07550.03320.31370.09630.287639.056-63.865519.0155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 350 )
3X-RAY DIFFRACTION3chain 'A' and (resid 351 through 441 )
4X-RAY DIFFRACTION4chain 'A' and (resid 442 through 481 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 89 )
7X-RAY DIFFRACTION7chain 'B' and (resid 90 through 237 )
8X-RAY DIFFRACTION8chain 'B' and (resid 238 through 265 )
9X-RAY DIFFRACTION9chain 'B' and (resid 266 through 384 )
10X-RAY DIFFRACTION10chain 'B' and (resid 385 through 422 )
11X-RAY DIFFRACTION11chain 'B' and (resid 423 through 466 )
12X-RAY DIFFRACTION12chain 'B' and (resid 467 through 482 )
13X-RAY DIFFRACTION13chain 'C' and (resid -2 through 24 )
14X-RAY DIFFRACTION14chain 'C' and (resid 25 through 237 )
15X-RAY DIFFRACTION15chain 'C' and (resid 238 through 265 )
16X-RAY DIFFRACTION16chain 'C' and (resid 266 through 350 )
17X-RAY DIFFRACTION17chain 'C' and (resid 351 through 440 )
18X-RAY DIFFRACTION18chain 'C' and (resid 441 through 482 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 24 )
20X-RAY DIFFRACTION20chain 'D' and (resid 25 through 89 )
21X-RAY DIFFRACTION21chain 'D' and (resid 90 through 237 )
22X-RAY DIFFRACTION22chain 'D' and (resid 238 through 265 )
23X-RAY DIFFRACTION23chain 'D' and (resid 266 through 288 )
24X-RAY DIFFRACTION24chain 'D' and (resid 289 through 350 )
25X-RAY DIFFRACTION25chain 'D' and (resid 351 through 384 )
26X-RAY DIFFRACTION26chain 'D' and (resid 385 through 422 )
27X-RAY DIFFRACTION27chain 'D' and (resid 423 through 441 )
28X-RAY DIFFRACTION28chain 'D' and (resid 442 through 481 )

+
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