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- PDB-3ffs: The Crystal Structure of Cryptosporidium parvum Inosine-5'-Monoph... -

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Basic information

Entry
Database: PDB / ID: 3ffs
TitleThe Crystal Structure of Cryptosporidium parvum Inosine-5'-Monophosphate Dehydrogenase
ComponentsInosine-5-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / beta-alpha barrel / TIM fold
Function / homology
Function and homology information


IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / GTP biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 Å
AuthorsRiera, T.V. / D'Aquino, J.A. / Lu, J. / Petsko, G.A. / Hedstrom, L.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: The structural basis of Cryptosporidium -specific IMP dehydrogenase inhibitor selectivity
Authors: Macpherson, I.S. / Kirubakaran, S. / Gorla, S.K. / Riera, T.V. / D'Aquino, J.A. / Zhang, M. / Cuny, G.D. / Hedstrom, L.
History
DepositionDec 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_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


Theoretical massNumber of molelcules
Total (without water)172,5374
Polymers172,5374
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-61 kcal/mol
Surface area47310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.068, 153.319, 98.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12B
22A
32C
42D
13C
23A
33B
43D
14D
24A
34B
44C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 6 / Auth seq-ID: 3 - 378 / Label seq-ID: 3 - 378

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
31CC
41DD
12BB
22AA
32CC
42DD
13CC
23AA
33BB
43DD
14DD
24AA
34BB
44CC

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Inosine-5-monophosphate dehydrogenase


Mass: 43134.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: IMPDH, 56k.02 / Plasmid: pTacTac / Production host: Escherichia coli (E. coli) / Strain (production host): TX685 / References: UniProt: Q8T6T2, IMP dehydrogenase

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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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein solution: 4 mg/mL IMPDH, 50 mM Tris, pH 7.5, 150 mM KCl, 5 % glycerol and 2 mM dithiothreitol. Well solution: 34 % PEG 4000, 25 mM sodium acetate and 100 mM Tris-Cl, pH 8.5. Combined ...Details: Protein solution: 4 mg/mL IMPDH, 50 mM Tris, pH 7.5, 150 mM KCl, 5 % glycerol and 2 mM dithiothreitol. Well solution: 34 % PEG 4000, 25 mM sodium acetate and 100 mM Tris-Cl, pH 8.5. Combined in a 1:1 ratio. VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2006
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 30575 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.179 / Χ2: 1.171
Reflection shellResolution: 3.19→3.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.632 / Num. unique all: 2987 / Χ2: 1.072 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EEP

1eep


Resolution: 3.19→48.34 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.82 / WRfactor Rfree: 0.313 / WRfactor Rwork: 0.259 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.953 / SU B: 26.148 / SU ML: 0.45 / SU Rfree: 0.58 / Cross valid method: THROUGHOUT / ESU R Free: 0.58
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1536 5 %RANDOM
Rwork0.269 ---
obs0.272 30483 99.08 %-
all-30575 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 84.19 Å2 / Biso mean: 53.887 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.19→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8561 0 0 0 8561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228634
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.97311684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23951180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38925.551263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.72151471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2711528
X-RAY DIFFRACTIONr_chiral_restr0.0920.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026114
X-RAY DIFFRACTIONr_nbd_refined0.2350.23854
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.222
X-RAY DIFFRACTIONr_mcbond_it0.4091.55995
X-RAY DIFFRACTIONr_mcangle_it0.73729338
X-RAY DIFFRACTIONr_scbond_it0.73732920
X-RAY DIFFRACTIONr_scangle_it1.2524.52346
Refine LS restraints NCS

Number: 1614 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
11ALOOSE POSITIONAL0.545
12BLOOSE POSITIONAL0.565
13CLOOSE POSITIONAL0.585
14DLOOSE POSITIONAL0.655
11ALOOSE THERMAL3.7510
12BLOOSE THERMAL1.5610
13CLOOSE THERMAL210
14DLOOSE THERMAL3.6310
21BLOOSE POSITIONAL0.565
22ALOOSE POSITIONAL0.545
23CLOOSE POSITIONAL0.585
24DLOOSE POSITIONAL0.655
21BLOOSE THERMAL1.5610
22ALOOSE THERMAL3.7510
23CLOOSE THERMAL210
24DLOOSE THERMAL3.6310
31CLOOSE POSITIONAL0.585
32ALOOSE POSITIONAL0.545
33BLOOSE POSITIONAL0.565
34DLOOSE POSITIONAL0.655
31CLOOSE THERMAL210
32ALOOSE THERMAL3.7510
33BLOOSE THERMAL1.5610
34DLOOSE THERMAL3.6310
41DLOOSE POSITIONAL0.655
42ALOOSE POSITIONAL0.545
43BLOOSE POSITIONAL0.565
44CLOOSE POSITIONAL0.585
41DLOOSE THERMAL3.6310
42ALOOSE THERMAL3.7510
43BLOOSE THERMAL1.5610
44CLOOSE THERMAL210
LS refinement shellResolution: 3.19→3.268 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 102 -
Rwork0.332 1888 -
all-1990 -
obs--89.88 %

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