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

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Basic information

Entry
Database: PDB / ID: 3tsd
TitleCrystal Structure of Inosine-5'-monophosphate Dehydrogenase from Bacillus anthracis str. Ames complexed with XMP
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / TIM barrel / CBS domain / cytosol / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
D(-)-TARTARIC ACID / XANTHOSINE-5'-MONOPHOSPHATE / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 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 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Sep 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)111,3436
Polymers110,3662
Non-polymers9774
Water1,71195
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)222,1948
Polymers220,7334
Non-polymers1,4614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area17260 Å2
ΔGint-101 kcal/mol
Surface area71380 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)223,17816
Polymers220,7334
Non-polymers2,44512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area19340 Å2
ΔGint-168 kcal/mol
Surface area77550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.250, 123.250, 141.636
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: pMCG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q81W29, UniProt: A0A6L8P2U9*PLUS, IMP dehydrogenase
#2: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE / Xanthosine monophosphate


Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O9P
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8 M sodium/potassium tartrate tetrahydrate, 0.1 M Tris pH8.5, 0.5 % PEGMME 5000, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2011 / 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: 2.65→50 Å / Num. all: 30553 / Num. obs: 30553 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 56.56 Å2 / Rsym value: 0.094 / Net I/σ(I): 10.4
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1502 / Rsym value: 0.735 / % possible all: 100

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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: 2.653→38.975 Å / SU ML: 0.6 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1474 5.07 %random
Rwork0.192 ---
all0.195 29052 --
obs0.195 29052 94.95 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.99 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 82.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.2593 Å2-0 Å20 Å2
2---2.2593 Å2-0 Å2
3---4.5187 Å2
Refinement stepCycle: LAST / Resolution: 2.653→38.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 0 63 95 6667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096653
X-RAY DIFFRACTIONf_angle_d1.2758982
X-RAY DIFFRACTIONf_dihedral_angle_d16.0152463
X-RAY DIFFRACTIONf_chiral_restr0.081065
X-RAY DIFFRACTIONf_plane_restr0.0071143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6531-2.73880.33071280.24642296242487
2.7388-2.83660.30091510.23312275242689
2.8366-2.95020.27641230.21942452257592
2.9502-3.08440.30171200.2112474259494
3.0844-3.24690.28411360.22512516265296
3.2469-3.45020.29941250.21072564268997
3.4502-3.71640.24781150.2022509262495
3.7164-4.09010.24691300.1692549267996
4.0901-4.68110.19531360.15432653278999
4.6811-5.89440.20911720.18326252797100
5.8944-38.97930.24141380.19172665280399
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)
11.4264-0.45810.21471.0605-0.72281.562-0.1131-0.1359-0.22680.1054-0.0516-0.06220.08460.16360.1090.41570.04960.03080.3259-0.04380.4082-38.409635.6772-3.1206
22.42510.7797-0.7383.126-0.88077.13210.056-0.5359-0.0670.52190.1616-0.4315-0.08030.8775-0.15860.6550.0350.12680.64570.08410.583-20.201212.257415.0854
30.9095-1.18640.49312.918-1.12472.8007-0.0370.1498-0.06920.11360.0708-0.03460.2150.06450.11910.36920.0370.07930.5715-0.03460.4703-28.961825.1169-1.7459
42.64820.43970.30954.893-0.3380.0697-0.14-0.0926-0.0240.10810.1699-0.15740.040.16970.07110.38420.00850.07540.38370.01310.2816-38.755147.0883-12.8513
52.5740.9681-1.66753.2343-3.33813.74060.5458-1.04570.31331.5372-0.38590.2422-1.17460.90010.08540.3780.08210.12720.1948-0.08840.3768-45.383541.82683.6539
64.2214-0.67732.82084.2465-2.74313.636-0.27820.0985-0.66520.40690.37990.8504-0.2823-0.132-0.06470.3229-0.00470.2110.3898-0.09020.4764-57.522538.4462-7.4205
72.4918-0.9064-1.25412.3090.73532.3338-0.12840.1377-0.33570.1362-0.1247-0.02230.16-0.2040.22570.3165-0.0148-0.1050.26730.10060.2413-56.899136.695547.9755
82.323-2.0509-1.77482.86361.02671.64020.1547-0.0538-0.3763-0.2927-0.2846-0.04240.08770.46480.11240.9186-0.124-0.02080.7531-0.0241.0392-44.1460.941626.5048
92.5898-2.0452-1.55931.54211.40712.2528-0.13960.3467-0.57640.068-0.18510.29150.4584-0.160.3570.6123-0.1120.06020.48260.10120.7514-51.31915.850442.3876
103.66250.2149-0.52552.7855-0.53152.0755-0.06040.55080.1797-0.1986-0.0334-0.12980.2014-0.16750.12870.20310.00710.01970.21180.07970.1543-53.149840.397741.6933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -3:107)
2X-RAY DIFFRACTION2chain 'A' and (resseq 108:170)
3X-RAY DIFFRACTION3chain 'A' and (resseq 171:270)
4X-RAY DIFFRACTION4chain 'A' and (resseq 271:334)
5X-RAY DIFFRACTION5chain 'A' and (resseq 335:427)
6X-RAY DIFFRACTION6chain 'A' and (resseq 428:473)
7X-RAY DIFFRACTION7chain 'B' and (resseq -9:77)
8X-RAY DIFFRACTION8chain 'B' and (resseq 78:152)
9X-RAY DIFFRACTION9chain 'B' and (resseq 153:309)
10X-RAY DIFFRACTION10chain 'B' and (resseq 310:472)

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