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- PDB-3tsb: Crystal Structure of Inosine-5'-monophosphate Dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 3tsb
TitleCrystal Structure of Inosine-5'-monophosphate Dehydrogenase from Bacillus anthracis str. Ames
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 / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
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
PHOSPHATE ION / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.595 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / 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
DepositionSep 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Feb 8, 2017Group: Structure summary
Revision 1.3Sep 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6515
Polymers110,3662
Non-polymers2853
Water2,234124
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)221,49212
Polymers220,7334
Non-polymers7608
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 area23200 Å2
ΔGint-149 kcal/mol
Surface area74040 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)221,1138
Polymers220,7334
Non-polymers3804
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 area21940 Å2
ΔGint-139 kcal/mol
Surface area69760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.026, 123.026, 140.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Detailstetramer is formed from either chain A or chain B by applying x,y,z; -y,x,z; y,-x,z; -x,-y,z

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Components

#1: Protein Inosine-5'-monophosphate dehydrogenase


Mass: 55183.172 Da / Num. of mol.: 2 / Fragment: IMPDH / Mutation: full-length
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: guaB, BAS0011, BA_0008, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 1.0 M NaH2PO4/K2HPO4 pH 8.2, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.595→50 Å / Num. all: 31165 / Num. obs: 31165 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 49.54 Å2 / Rsym value: 0.095 / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1554 / Rsym value: 0.725 / % possible all: 98.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: dev_851)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1ZFJ monomer

1zfj


Resolution: 2.595→36.997 Å / SU ML: 0.57 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1580 5.09 %random
Rwork0.181 ---
all0.184 31065 --
obs0.184 31065 96.01 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.356 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 61.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.1357 Å20 Å2-0 Å2
2--1.1357 Å20 Å2
3----2.2713 Å2
Refinement stepCycle: LAST / Resolution: 2.595→36.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6943 0 15 124 7082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017064
X-RAY DIFFRACTIONf_angle_d1.329539
X-RAY DIFFRACTIONf_dihedral_angle_d15.4882636
X-RAY DIFFRACTIONf_chiral_restr0.0991109
X-RAY DIFFRACTIONf_plane_restr0.0071232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.5947-2.67850.30521370.2338X-RAY DIFFRACTION262890
2.6785-2.77420.29971410.2175X-RAY DIFFRACTION283597
2.7742-2.88520.30851510.21X-RAY DIFFRACTION285298
2.8852-3.01640.30951410.2175X-RAY DIFFRACTION289998
3.0164-3.17540.28511520.2098X-RAY DIFFRACTION286198
3.1754-3.37420.26681400.1967X-RAY DIFFRACTION284897
3.3742-3.63450.25921410.1814X-RAY DIFFRACTION286697
3.6345-3.99990.24741590.1559X-RAY DIFFRACTION283697
3.9999-4.57780.18031320.1375X-RAY DIFFRACTION282696
4.5778-5.7640.20311410.1625X-RAY DIFFRACTION280295
5.764-37.0010.22421450.1947X-RAY DIFFRACTION281294
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)
11.48950.1736-0.19460.6937-0.08290.9758-0.0171-0.051-0.14840.05640.01120.09410.1533-0.0344-0.00810.3456-0.0153-0.05090.3578-0.03610.3446-29.2624-27.2246-19.041
22.801-0.34250.04962.6543-0.53083.286-0.1337-0.5874-0.18260.6660.40060.25680.2933-0.8004-0.22320.7225-0.01850.0490.82390.02910.6226-51.9572-40.4576-1.1581
32.93321.8604-1.24573.3657-1.36011.7817-0.11020.06530.3473-0.01340.29850.82660.2402-0.4472-0.19110.4545-0.0359-0.0440.59220.03380.5717-49.6411-29.6779-15.306
40.8086-0.1284-0.40641.5956-0.02970.44740.04160.0491-0.1260.101-0.00680.08560.20220.029-0.01390.326-0.0081-0.05080.2707-0.00960.2845-16.8586-26.4924-29.4766
52.8125-0.305-0.48383.6851-0.31791.9957-0.0003-0.6877-0.21150.4970.1161-0.4190.39610.3819-0.13260.46660.0056-0.05310.5002-0.05070.4277-16.6429-19.724-13.1275
62.65730.4362-0.18442.6976-0.98741.84560.2046-0.2445-0.0020.4016-0.11120.0708-0.16380.0374-0.1050.42730.0528-0.05880.40910.0040.422-18.8065-0.4632-23.9038
71.2655-0.1243-0.29961.2179-1.37361.5502-0.0082-0.1840.26560.03860.2189-0.224-0.61590.1358-0.11620.39130.0236-0.02470.43280.00460.3455-11.61469.889941.9281
84.0934-0.77660.63622.6696-0.55682.6783-0.0151-0.1083-0.3623-0.03660.01310.41640.3114-0.35240.01530.3663-0.05490.02610.40720.02890.3822-29.289-15.330725.5739
92.97840.44111.62551.22650.64762.4016-0.11140.47230.2089-0.44570.17130.7387-0.1582-0.7355-0.04510.4241-0.014-0.04170.70610.11870.5953-45.0999-8.472813.6049
102.0613-0.08180.58542.3538-0.42841.78970.2088-0.02970.22830.5026-0.29310.67950.0291-0.3940.04440.9161-0.12840.33171.0211-0.02551.0378-58.973-30.528812.6925
112.04621.94381.54035.85580.23355.1735-0.92191.174-0.9962-0.50720.6620.6489-0.0974-0.95980.36290.7737-0.02530.06720.8025-0.08640.783-52.6687-27.397413.5684
120.68080.17420.94632.44820.85182.2865-0.12-0.050.2440.0808-0.04690.7174-0.2644-0.57150.16020.31740.05970.05130.49840.02320.4956-37.96851.361327.6002
132.66480.65921.09073.26460.34532.09650.04990.38480.2698-0.54810.05760.262-0.4747-0.3042-0.14770.41660.06760.05450.45640.04080.4443-24.68931.086819.3468
142.82110.36251.37721.40080.58052.9733-0.14760.351-0.1681-0.2382-0.0610.0827-0.03560.40360.18350.37310.02410.03250.36720.01760.4476-15.9491-14.880120.5602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -3:133)
2X-RAY DIFFRACTION2chain 'A' and (resseq 134:170)
3X-RAY DIFFRACTION3chain 'A' and (resseq 171:223)
4X-RAY DIFFRACTION4chain 'A' and (resseq 224:355)
5X-RAY DIFFRACTION5chain 'A' and (resseq 356:446)
6X-RAY DIFFRACTION6chain 'A' and (resseq 447:486)
7X-RAY DIFFRACTION7chain 'B' and (resseq -8:18)
8X-RAY DIFFRACTION8chain 'B' and (resseq 19:56)
9X-RAY DIFFRACTION9chain 'B' and (resseq 57:139)
10X-RAY DIFFRACTION10chain 'B' and (resseq 140:180)
11X-RAY DIFFRACTION11chain 'B' and (resseq 181:209)
12X-RAY DIFFRACTION12chain 'B' and (resseq 210:309)
13X-RAY DIFFRACTION13chain 'B' and (resseq 310:418)
14X-RAY DIFFRACTION14chain 'B' and (resseq 419:486)

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