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- PDB-3usb: Crystal Structure of Bacillus anthracis Inosine Monophosphate Deh... -

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Basic information

Entry
Database: PDB / ID: 3usb
TitleCrystal Structure of Bacillus anthracis Inosine Monophosphate Dehydrogenase in the complex with IMP
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / CBS-domain / cytosol
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
INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.38 Å
AuthorsKim, Y. / Zhang, R. / Wu, R. / Gu, M. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Biochemistry / Year: 2012
Title: Bacillus anthracis inosine 5'-monophosphate dehydrogenase in action: the first bacterial series of structures of phosphate ion-, substrate-, and product-bound complexes.
Authors: Makowska-Grzyska, M. / Kim, Y. / Wu, R. / Wilton, R. / Gollapalli, D.R. / Wang, X.K. / Zhang, R. / Jedrzejczak, R. / Mack, J.C. / Maltseva, N. / Mulligan, R. / Binkowski, T.A. / Gornicki, P. ...Authors: Makowska-Grzyska, M. / Kim, Y. / Wu, R. / Wilton, R. / Gollapalli, D.R. / Wang, X.K. / Zhang, R. / Jedrzejczak, R. / Mack, J.C. / Maltseva, N. / Mulligan, R. / Binkowski, T.A. / Gornicki, P. / Kuhn, M.L. / Anderson, W.F. / Hedstrom, L. / Joachimiak, A.
History
DepositionNov 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Source and taxonomy
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,25311
Polymers111,9612
Non-polymers1,2929
Water7,494416
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)226,43520
Polymers223,9224
Non-polymers2,51416
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 area18760 Å2
ΔGint-165 kcal/mol
Surface area72860 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)226,57724
Polymers223,9224
Non-polymers2,65620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area19860 Å2
ΔGint-244 kcal/mol
Surface area70900 Å2
MethodPISA
3
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

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)453,01344
Polymers447,8438
Non-polymers5,16936
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_555x+1/2,y+1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_555-y+1/2,x+1/2,z+1/21
crystal symmetry operation8_555y+1/2,-x+1/2,z+1/21
Buried area46730 Å2
ΔGint-436 kcal/mol
Surface area135650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.519, 122.519, 140.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inosine-5'-monophosphate dehydrogenase


Mass: 55980.383 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 425 molecules

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


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 20% (w/v) PEG3350, 0.2 M, magnessium sulfate, 0.1 M TrisHCl pH 7.6, 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: 0.97959 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 41552 / Num. obs: 41552 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 27.59 Å2 / Rsym value: 0.07 / Net I/σ(I): 12.9
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 3.33 / Num. unique all: 2105 / Rsym value: 0.776 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_851)refinement
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.38→38.744 Å / SU ML: 0.58 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2058 5.03 %random
Rwork0.17 ---
all0.172 40903 --
obs0.172 40903 98.32 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.244 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.4611 Å20 Å2-0 Å2
2--0.4611 Å20 Å2
3----0.9222 Å2
Refinement stepCycle: LAST / Resolution: 2.38→38.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6314 0 81 416 6811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116578
X-RAY DIFFRACTIONf_angle_d1.418909
X-RAY DIFFRACTIONf_dihedral_angle_d15.4192449
X-RAY DIFFRACTIONf_chiral_restr0.1021057
X-RAY DIFFRACTIONf_plane_restr0.0081137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.38-2.43580.25841020.19242143224581
2.4358-2.49670.26631120.20882541265396
2.4967-2.56420.23731440.189426172761100
2.5642-2.63970.23341630.181225782741100
2.6397-2.72490.21391490.178226422791100
2.7249-2.82220.19011170.174626312748100
2.8222-2.93520.2291360.167326402776100
2.9352-3.06870.23611420.179226192761100
3.0687-3.23040.23441420.17726192761100
3.2304-3.43270.21051350.174926342769100
3.4327-3.69760.19511380.166626292767100
3.6976-4.06930.19471290.152826402769100
4.0693-4.65730.16421500.138226552805100
4.6573-5.86440.17381390.16726482787100
5.8644-38.7490.17631600.18512609276998
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)
11.8679-1.2491-1.01564.09690.15050.5853-0.3036-0.38510.0710.79390.0611-0.4433-0.00590.05610.25370.2344-0.0583-0.05350.1445-0.03590.180114.45720.0455130.9845
22.16470.9727-0.48761.6648-0.5761.065-0.03760.31710.23-0.334-0.0123-0.1588-0.13570.04160.02050.2403-0.0183-0.01360.14910.02130.188730.366434.872107.3449
32.71460.48870.62020.65171.55884.2139-0.1251.23980.4182-1.59520.02840.0374-0.63090.44080.04851.0355-0.03670.01680.6260.12960.46241.556651.31290.2217
41.73871.5178-0.47742.5329-0.71782.15070.00830.15750.32240.05710.05320.0531-0.5740.1161-0.03340.2756-0.04550.00490.163-0.00620.246632.520144.0903109.4262
52.4740.8354-0.84323.396-1.06290.824-0.11780.0042-0.2142-0.1289-0.0624-0.28810.12820.01740.06990.1502-0.0213-0.05650.1227-0.0330.202230.411417.1694122.6446
61.3481-0.87-0.48172.5339-0.45860.307-0.00420.00570.0941-0.1014-0.010.0927-0.0690.0564-0.00230.1084-0.0258-0.03110.0988-0.02630.115715.725316.0683121.0327
73.9648-0.6410.24453.75540.0314.50310.43771.5897-1.8729-1.3578-0.16190.84381.0387-0.3062-0.06180.66540.0219-0.30870.7691-0.4254-0.426317.191921.004894.9454
82.52150.377-1.81982.276-2.12853.0081-0.14640.11310.1186-0.06960.12960.2249-0.0326-0.2938-0.02610.11790.0128-0.05830.1396-0.06690.20375.08724.0149119.0458
90.5912-0.60840.30922.29791.70532.17680.49350.6171-0.0043-0.4466-0.12-0.1654-0.39270.0503-0.31330.22660.0402-0.00550.28460.0080.130374.968449.3931118.4712
101.01990.4682-0.40862.8822-0.04171.33420.1231-0.3678-0.2790.2584-0.1382-0.0770.3214-0.1109-0.0260.2481-0.0947-0.10220.21340.08210.194949.48930.9097140.6131
110.21510.3464-0.33910.9863-0.43570.1636-0.4196-0.4266-1.08380.1228-0.3851-0.04730.6037-0.3630.23730.9247-0.1143-0.1468-0.2390.7860.782849.63275.3528149.4327
121.18070.8594-1.80831.8351-0.30052.246-0.2824-0.3243-0.80490.1614-0.1519-0.44530.5888-0.0950.20630.38560.006-0.08260.19670.13050.473850.324714.7317141.1142
132.88670.4802-0.04621.4123-0.3330.50290.1294-0.50020.02820.2239-0.07480.02740.0754-0.0708-0.03760.1953-0.0459-0.0330.1953-0.03050.113352.515839.6155140.1548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq -6:18)A-6 - 18
2X-RAY DIFFRACTION2chain 'A' and (resseq 19:133)A19 - 133
3X-RAY DIFFRACTION3chain 'A' and (resseq 134:163)A134 - 163
4X-RAY DIFFRACTION4chain 'A' and (resseq 164:242)A164 - 242
5X-RAY DIFFRACTION5chain 'A' and (resseq 243:309)A243 - 309
6X-RAY DIFFRACTION6chain 'A' and (resseq 310:363)A310 - 363
7X-RAY DIFFRACTION7chain 'A' and (resseq 364:427)A364 - 427
8X-RAY DIFFRACTION8chain 'A' and (resseq 428:469)A428 - 469
9X-RAY DIFFRACTION9chain 'B' and (resseq -7:12)B-7 - 12
10X-RAY DIFFRACTION10chain 'B' and (resseq 13:77)B13 - 77
11X-RAY DIFFRACTION11chain 'B' and (resseq 78:125)B78 - 125
12X-RAY DIFFRACTION12chain 'B' and (resseq 137:309)B137 - 309
13X-RAY DIFFRACTION13chain 'B' and (resseq 310:469)B310 - 469

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