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- PDB-4mjm: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, ... -

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Basic information

Entry
Database: PDB / ID: 4mjm
TitleCrystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Short Internal Deletion of CBS Domain from Bacillus anthracis str. Ames
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / alpha-beta fold / Hydrolase
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP 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
Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2544 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2013
Title: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Short Internal Deletion of CBS Domain from Bacillus anthracis str. Ames
Authors: Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Sep 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)163,52412
Polymers163,0274
Non-polymers4978
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13230 Å2
ΔGint-63 kcal/mol
Surface area53360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.328, 84.249, 84.313
Angle α, β, γ (deg.)110.01, 109.22, 109.19
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 40756.746 Da / Num. of mol.: 4 / Fragment: IMPDH-S, Apo form
Mutation: Short internal deletion of CBS domain (95-200) and Gly is inserted at 95
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 Magic
References: UniProt: Q81W29, UniProt: A0A6L8P2U9*PLUS, IMP dehydrogenase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 289 K / pH: 6.5
Details: 0.2 M sodium chloride, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate , 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: 0.97921
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
Reflection twinOperator: -h-k-l,l,k / Fraction: 0.5
ReflectionResolution: 2.25→50 Å / Num. obs: 79311 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 36.1 Å2 / Rsym value: 0.052 / Net I/σ(I): 12.7
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.17 / Rsym value: 0.485 / % possible all: 96.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TSD

3tsd


Resolution: 2.2544→48.832 Å / Isotropic thermal model: mixed / σ(F): 1.96 / Phase error: 27.48 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2323 4055 5.11 %
Rwork0.2064 --
obs0.2094 79280 94.1 %
all-87137 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2544→48.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9632 0 32 464 10128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049775
X-RAY DIFFRACTIONf_angle_d0.85413176
X-RAY DIFFRACTIONf_dihedral_angle_d15.6023596
X-RAY DIFFRACTIONf_chiral_restr0.0551571
X-RAY DIFFRACTIONf_plane_restr0.0041700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2544-2.29320.41121780.40473564X-RAY DIFFRACTION85
2.2932-2.33490.34522110.34113891X-RAY DIFFRACTION93
2.3349-2.37980.35322190.31853891X-RAY DIFFRACTION92
2.3798-2.42840.33192130.29323901X-RAY DIFFRACTION93
2.4284-2.48120.33761930.28213975X-RAY DIFFRACTION93
2.4812-2.53880.28031930.28193897X-RAY DIFFRACTION93
2.5388-2.60230.28841870.27193894X-RAY DIFFRACTION93
2.6023-2.67260.2672080.27143920X-RAY DIFFRACTION93
2.6726-2.75120.26131970.25513983X-RAY DIFFRACTION93
2.7512-2.840.27952140.26273895X-RAY DIFFRACTION93
2.84-2.94140.28452340.24353946X-RAY DIFFRACTION93
2.9414-3.05910.26612160.24483887X-RAY DIFFRACTION93
3.0591-3.19810.25932050.22443910X-RAY DIFFRACTION93
3.1981-3.36650.24422330.2194014X-RAY DIFFRACTION93
3.3665-3.57720.25581650.20913301X-RAY DIFFRACTION80
3.5772-3.85290.22561170.18212464X-RAY DIFFRACTION58
3.8529-4.23970.16651740.15763166X-RAY DIFFRACTION75
4.2397-4.85110.17721980.13843902X-RAY DIFFRACTION93
4.8511-6.10390.17331960.16393930X-RAY DIFFRACTION93
6.1039-30.60260.18822000.15853988X-RAY DIFFRACTION94
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)
11.128-0.21630.8924-0.0288-0.42960.6052-0.09760.504-0.19270.13490.0859-0.2934-0.2104-0.1978-0.02040.32080.06060.09620.3858-0.10770.3383-15.21588.7136-7.1077
21.5601-0.72330.38135.0404-1.57953.2189-0.232-0.10030.15080.2499-0.0059-0.47710.0178-0.02460.25040.28540.0627-0.03870.2394-0.00120.238511.26031.11471.9214
33.58670.71050.99651.23050.63780.99620.071-0.1487-0.03040.0906-0.05610.05980.2001-0.1472-0.03180.2970.0586-0.02910.27010.05840.1879-7.1728-2.46414.5568
41.5973-0.19990.66990.22620.58441.4954-0.0546-0.0702-0.212-0.25590.12560.1606-0.22110.049-0.08920.37880.07250.01690.27130.08750.2904-2.10163.3911-13.3767
51.70410.6364-0.85162.3320.89710.8668-0.1964-0.2658-0.17140.07240.25570.19540.2437-0.0577-0.11040.29430.07250.0260.2850.03240.3442-34.27337.6068-18.4136
62.9869-0.09811.4950.549-0.08452.8204-0.01510.37540.1883-0.05190.07710.0055-0.20710.0297-0.02110.37330.0258-0.03850.24480.04530.2598-25.269426.2591-43.017
77.38870.2707-0.30317.8805-1.35166.8082-0.1938-0.0553-0.0230.08230.0241-1.5291-0.19260.6050.3130.4419-0.023-0.05470.2349-0.07130.5598-12.255833.8663-32.2229
84.74920.33610.86532.46891.14496.8235-0.0269-0.24-0.27750.65930.1646-0.41150.1386-0.1138-0.11130.40560.0129-0.13210.243-0.05140.4303-17.059331.0598-24.2829
91.3642-0.0565-1.16013.9268-0.00632.158-0.26060.00090.11670.58230.3267-0.43180.07970.109-0.12250.35830.0205-0.03480.2797-0.00880.2222-22.191123.8444-22.0694
101.6303-0.5253-0.48742.0406-1.04061.18130.02270.10550.03660.02290.06990.01160.2266-0.0596-0.07810.30410.0329-0.04290.26190.03950.1881-28.160414.6647-25.0085
114.14041.15580.04253.9351-0.21042.1048-0.24650.731-0.9048-0.6141-0.1495-0.30440.470.27640.30240.61030.0756-0.00050.3850.02670.3711-18.88938.6418-47.7001
121.47440.32670.32452.583-1.31732.2483-0.26950.15320.19130.304-0.2038-0.2067-0.3507-0.02830.45080.31460.0563-0.03480.27630.02990.2324-40.43158.3502-27.4355
130.85210.0698-0.19481.743-1.49591.22310.4531-0.87240.66120.5066-0.04620.3019-0.0195-0.0982-0.17140.6283-0.0127-0.29080.42690.38040.248-42.9042-10.4495-15.1923
141.95541.0320.5357-0.0279-0.01453.1430.01420.29170.0401-0.19050.14490.220.1638-0.0026-0.09610.4380.0632-0.11560.29340.06370.35-58.0315-20.1131-41.3519
151.6138-0.33612.24263.0010.79574.4685-0.1666-0.08210.0699-0.24930.17920.0158-0.3268-0.37460.05720.32630.10350.00140.34360.08420.3715-57.2374-4.0044-33.5949
162.96450.09730.82780.70310.89131.3764-0.1246-0.20250.08320.2330.0499-0.1026-0.11390.18030.10630.4699-0.02990.00440.3660.1360.2494-47.4543-10.2047-24.1278
170.97021.14061.0121.8853-0.49875.21660.05120.1905-0.6136-0.33440.1941-0.31680.01591.3488-0.15680.34430.1022-0.03770.5571-0.06160.4919-40.832-23.9365-41.6835
182.3155-0.672-0.02621.7655-0.30762.64380.4627-0.0976-0.15210.2595-0.1494-0.39290.2955-0.0221-0.31680.4663-0.0479-0.19940.32560.18050.5129-44.9418-22.8631-19.1178
190.9322-0.0603-0.50330.82370.07710.32270.74680.047-0.08730.4069-0.32490.04730.53530.0534-0.43960.60440.0681-0.06980.49650.12180.2665-21.9065-17.86362.3011
200.97340.49510.59882.79693.3083.70620.21290.05060.0525-0.0319-0.159-0.27360.2137-0.1404-0.02390.34480.0795-0.0240.24820.05450.2769-23.1297-42.2401-1.5443
213.6890.30630.02551.9125-0.2743-0.01910.4923-0.1805-0.51140.2003-0.0484-0.47430.71770.2478-0.45270.50470.1023-0.08370.3070.01970.5274-17.976-53.25632.2736
224.32570.9592-0.80542.26521.05261.03440.1999-0.147-0.6370.6208-0.27170.31320.0074-0.12170.06750.53480.055-0.07110.22010.03280.3587-29.818-49.36491.7736
232.2383-1.60331.51897.813-0.03290.72490.12680.2435-0.2276-0.4362-0.07750.6967-0.06070.0728-0.01490.29050.0263-0.02990.38520.05370.2405-40.5857-39.01780.0784
241.41-0.0529-0.18972.2585-0.51971.36450.00540.2964-0.141-0.506-0.34790.1839-0.0638-0.29370.21160.36140.0578-0.08070.3814-0.0310.2822-28.7877-28.3923-4.3293
250.9419-0.747-0.54232.12010.0695-0.1480.1178-0.03410.1854-0.2253-0.0115-0.11170.01110.2389-0.04570.3880.026-0.07150.32650.06560.3492-15.5319-26.9418-5.3142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 257 )
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 363 )
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 470 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 28 )
6X-RAY DIFFRACTION6chain 'B' and (resid 29 through 223 )
7X-RAY DIFFRACTION7chain 'B' and (resid 224 through 242 )
8X-RAY DIFFRACTION8chain 'B' and (resid 243 through 270 )
9X-RAY DIFFRACTION9chain 'B' and (resid 271 through 311 )
10X-RAY DIFFRACTION10chain 'B' and (resid 312 through 367 )
11X-RAY DIFFRACTION11chain 'B' and (resid 368 through 437 )
12X-RAY DIFFRACTION12chain 'B' and (resid 438 through 469 )
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 28 )
14X-RAY DIFFRACTION14chain 'C' and (resid 29 through 257 )
15X-RAY DIFFRACTION15chain 'C' and (resid 258 through 310 )
16X-RAY DIFFRACTION16chain 'C' and (resid 311 through 356 )
17X-RAY DIFFRACTION17chain 'C' and (resid 357 through 427 )
18X-RAY DIFFRACTION18chain 'C' and (resid 428 through 470 )
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 33 )
20X-RAY DIFFRACTION20chain 'D' and (resid 34 through 77 )
21X-RAY DIFFRACTION21chain 'D' and (resid 78 through 210 )
22X-RAY DIFFRACTION22chain 'D' and (resid 211 through 243 )
23X-RAY DIFFRACTION23chain 'D' and (resid 244 through 293 )
24X-RAY DIFFRACTION24chain 'D' and (resid 294 through 375 )
25X-RAY DIFFRACTION25chain 'D' and (resid 376 through 472 )

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