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- PDB-4qm1: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase w... -

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Basic information

Entry
Database: PDB / ID: 4qm1
TitleCrystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor D67
ComponentsInosine-5'-monophosphate dehydrogenase
Keywordsoxidoreductase/oxidoreductase inhibitor / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / alpha-beta structure / 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-39H / 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: 2.7964 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Mandapati, K. / Gollapalli, D. / Gorla, S.K. / Zhang, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. ...Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Mandapati, K. / Gollapalli, D. / Gorla, S.K. / Zhang, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2014
Title: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor D67
Authors: Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Mandapati, K. / Gollapalli, D. / Gorla, S.K. / Zhang, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionJun 14, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJul 23, 2014ID: 4MXS
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Structure summary
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 20, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)165,78112
Polymers162,8384
Non-polymers2,9438
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20710 Å2
ΔGint-112 kcal/mol
Surface area49070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.130, 101.331, 87.267
Angle α, β, γ (deg.)90.00, 109.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40709.574 Da / Num. of mol.: 4 / Fragment: IMPDH-delta-L-CBS / Mutation: CBS domain (residues 92-220) is replaced with GG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: guaB, BA_0008, BAS0011, GBAA_0008 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold
References: UniProt: Q81W29, UniProt: A0A6L8P2U9*PLUS, IMP dehydrogenase
#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-39H / 2-(3-methyl-4-oxo-3,4-dihydrophthalazin-1-yl)-N-(6,7,8,9-tetrahydrodibenzo[b,d]furan-2-yl)acetamide / D67


Mass: 387.431 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H21N3O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M magnessium chloride hexahydrate 0.1 M HEPES pH 7.5, 22% w/v Polyacrylic acid, sodium salt 5100, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.7964→50 Å / Num. all: 33129 / Num. obs: 33129 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 63.91 Å2 / Rsym value: 0.154 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7964→2.85 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.749 / % possible all: 93.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3TSD

3tsd


Resolution: 2.7964→40.946 Å / SU ML: 0.41 / Isotropic thermal model: mixed / σ(F): 1.34 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1681 5.09 %
Rwork0.192 --
obs0.1949 33022 97.55 %
all-33022 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7964→40.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9854 0 208 17 10079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110206
X-RAY DIFFRACTIONf_angle_d1.24213815
X-RAY DIFFRACTIONf_dihedral_angle_d16.1663712
X-RAY DIFFRACTIONf_chiral_restr0.0451615
X-RAY DIFFRACTIONf_plane_restr0.0051753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7964-2.87870.35041150.2962293X-RAY DIFFRACTION86
2.8787-2.97150.3471670.29842566X-RAY DIFFRACTION97
2.9715-3.07770.36191430.27632622X-RAY DIFFRACTION99
3.0777-3.20090.33951200.27482670X-RAY DIFFRACTION99
3.2009-3.34650.32381510.25062607X-RAY DIFFRACTION99
3.3465-3.52290.33031330.22122656X-RAY DIFFRACTION99
3.5229-3.74340.22591400.20182657X-RAY DIFFRACTION99
3.7434-4.03220.26841440.18232644X-RAY DIFFRACTION99
4.0322-4.43760.22931220.15912683X-RAY DIFFRACTION99
4.4376-5.07870.19991700.15112634X-RAY DIFFRACTION99
5.0787-6.39470.22341350.17952693X-RAY DIFFRACTION99
6.3947-40.95060.19041410.15392616X-RAY DIFFRACTION95
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)
17.17050.55554.24762.05910.60955.46590.40920.2404-0.5998-0.2217-0.1135-0.30510.53820.6282-0.29470.569-0.02020.05820.47-0.05550.609925.7834-14.497521.3111
23.66250.3689-2.63564.3462.96734.0296-0.21150.3424-0.2151-0.2814-0.1260.23590.1381-0.59540.35640.5605-0.0053-0.05340.51040.05760.4056-5.4642-14.40914.6931
35.17981.1087-0.9816.0926-0.11696.3129-0.0435-0.10070.5630.6411-0.07660.7208-0.263-0.28750.11440.4773-0.04490.0960.63240.00630.5167-16.5323-7.313922.6765
47.3136-0.032-2.42012.8649-0.29042.1282-0.242-0.3209-0.27740.24640.0217-0.12310.3633-0.24950.22230.5869-0.0451-0.02660.59860.01630.4543-2.413-16.631327.3271
50.37780.61640.31851.26591.15891.3391-0.05620.0864-0.1240.04590.0715-0.07420.0748-0.1262-0.00690.514-0.04770.00510.55250.01490.53773.3954-11.125312.9388
66.0529-0.12363.68263.10690.32195.9693-0.2174-0.13680.1717-0.10860.1576-0.0942-0.7258-0.50750.0130.75240.0353-0.04440.55250.0350.6263-6.44918.645713.6731
73.6828-2.05770.29092.99811.26923.4664-0.08760.1099-0.1825-0.21980.14970.03710.1788-0.1347-0.05840.5915-0.10170.05360.5866-0.00310.43410.9521-12.2556-2.308
87.26493.4777-5.42521.7967-3.00064.6240.21370.0421-0.1450.3252-0.1258-0.1248-0.2385-0.03830.03940.5838-0.0492-0.05170.4317-0.07030.416422.4525-13.9901-7.8866
95.50840.68160.68691.22850.51392.07770.00840.69850.0056-0.204-0.03340.2180.115-0.2570.06770.676-0.03380.04230.68250.02050.47857.3676-7.1755-34.5528
101.56050.1162-0.07241.19530.27681.6303-0.03740.1494-0.14810.1990.03030.28810.2685-0.09110.04080.5333-0.10390.01910.5176-0.0540.52368.5197-16.7236-22.127
115.0904-0.7814-1.78211.8769-0.19261.9150.2340.11030.4578-0.02680.02020.1279-0.3289-0.214-0.25130.7891-0.0040.05890.5854-0.00070.59228.38223.3387-23.3905
121.64540.1304-0.31062.6409-0.28931.7750.05450.1327-0.10470.0123-0.114-0.38950.0737-0.40760.02880.52820.01790.05610.71110.00780.48225.74611.1558-17.8267
130.3777-0.5701-0.4311.34410.15060.77870.08770.0456-0.0086-0.0964-0.0605-0.15920.0452-0.0681-0.03180.6731-0.0281-0.04940.57990.00690.550727.57980.543725.2103
146.17230.0858-1.72334.94430.25438.04470.4269-0.02580.63770.3104-0.2217-0.5942-0.907-0.1838-0.22350.694-0.0337-0.00230.5264-0.04930.637332.064921.649137.4351
150.996-2.393-2.25424.66463.01845.1388-0.001-0.2002-0.0783-0.09520.257-0.6012-0.02170.7734-0.25890.5237-0.0569-0.04720.7027-0.00410.676644.717713.270133.9616
161.38870.5467-0.85890.60430.37363.06870.10180.0583-0.01310.01650.0192-0.0240.0570.072-0.11460.51280.0093-0.0060.47690.01570.532633.95243.582724.7465
173.78480.141-1.92023.37940.57782.43570.45770.34280.7731-0.2192-0.1062-0.2424-0.1004-0.1232-0.42550.91810.12650.04130.71190.05260.872524.753624.762319.8434
184.1628-0.29580.01093.9588-0.65712.2456-0.1177-0.19190.0348-0.26940.14190.0806-0.0699-0.105-0.01380.4968-0.01760.00260.43350.0140.468316.7631-0.689125.3624
191.24910.3863-0.16941.2246-0.46910.5454-0.0194-0.21170.03380.049-0.05590.0126-0.0284-0.01260.06550.42710.0244-0.01830.4627-0.01040.483644.55494.1495-3.2706
207.3344-0.23470.74586.3133-0.26377.0791-0.16480.08640.6315-0.28790.40480.016-0.77430.1183-0.23810.4914-0.0485-0.01090.4659-0.02280.495952.0721.5516-18.6603
215.40463.24960.06936.8391-0.91472.17150.06030.7359-0.3579-0.47650.0740.08780.08670.3314-0.08550.65890.03950.1010.4951-0.07130.512852.630610.6907-23.5069
222.08380.2913-0.17171.29960.07982.125-0.0842-0.0389-0.1526-0.10180.0717-0.14430.11690.15940.0560.53220.0171-0.0010.45910.00290.511545.75460.9877-13.4451
234.1415-1.74421.59314.7996-0.41234.2143-0.00920.16660.1617-0.2189-0.00020.3429-0.3534-0.37120.03770.5253-0.01230.08230.5630.04240.532135.59220.5066-13.8981
246.7919-0.73260.44983.9481-6.05499.3935-0.1973-0.34210.82280.66840.0031-1.1658-0.95550.26730.02580.4722-0.0257-0.06690.4452-0.03250.505245.964816.65824.5589
250.18840.3975-1.17183.97170.75385.06320.30760.2458-0.0338-0.2082-0.04650.0893-0.1134-0.0863-0.23810.55120.0204-0.02420.47270.08420.467839.69754.5227.5445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 242 )
4X-RAY DIFFRACTION4chain 'A' and (resid 243 through 293 )
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 368 )
6X-RAY DIFFRACTION6chain 'A' and (resid 369 through 427 )
7X-RAY DIFFRACTION7chain 'A' and (resid 428 through 479 )
8X-RAY DIFFRACTION8chain 'B' and (resid -2 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 232 )
10X-RAY DIFFRACTION10chain 'B' and (resid 233 through 356 )
11X-RAY DIFFRACTION11chain 'B' and (resid 357 through 446 )
12X-RAY DIFFRACTION12chain 'B' and (resid 447 through 486 )
13X-RAY DIFFRACTION13chain 'C' and (resid -2 through 56 )
14X-RAY DIFFRACTION14chain 'C' and (resid 57 through 91 )
15X-RAY DIFFRACTION15chain 'C' and (resid 92 through 270 )
16X-RAY DIFFRACTION16chain 'C' and (resid 271 through 368 )
17X-RAY DIFFRACTION17chain 'C' and (resid 369 through 427 )
18X-RAY DIFFRACTION18chain 'C' and (resid 428 through 478 )
19X-RAY DIFFRACTION19chain 'D' and (resid -1 through 56 )
20X-RAY DIFFRACTION20chain 'D' and (resid 57 through 90 )
21X-RAY DIFFRACTION21chain 'D' and (resid 91 through 257 )
22X-RAY DIFFRACTION22chain 'D' and (resid 258 through 355 )
23X-RAY DIFFRACTION23chain 'D' and (resid 356 through 427 )
24X-RAY DIFFRACTION24chain 'D' and (resid 428 through 445 )
25X-RAY DIFFRACTION25chain 'D' and (resid 446 through 479 )

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