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- PDB-1eep: 2.4 A RESOLUTION CRYSTAL STRUCTURE OF BORRELIA BURGDORFERI INOSIN... -

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Basic information

Entry
Database: PDB / ID: 1eep
Title2.4 A RESOLUTION CRYSTAL STRUCTURE OF BORRELIA BURGDORFERI INOSINE 5'-MONPHOSPHATE DEHYDROGENASE IN COMPLEX WITH A SULFATE ION
ComponentsINOSINE 5'-MONOPHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALPHA-BETA BARREL / TIM BARREL / IMPDH / IMP DEHYDROGENASE / LOOP-6 / PURINE BIOSYNTHESIS
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / 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 / 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 speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsMcMillan, F.M. / Cahoon, M. / White, A. / Hedstrom, L. / Petsko, G.A. / Ringe, D.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structure at 2.4 A resolution of Borrelia burgdorferi inosine 5'-monophosphate dehydrogenase: evidence of a substrate-induced hinged-lid motion by loop 6.
Authors: McMillan, F.M. / Cahoon, M. / White, A. / Hedstrom, L. / Petsko, G.A. / Ringe, D.
History
DepositionFeb 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)87,8474
Polymers87,6552
Non-polymers1922
Water1,928107
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)175,6948
Polymers175,3104
Non-polymers3844
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 area11850 Å2
ΔGint-127 kcal/mol
Surface area46390 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)175,6948
Polymers175,3104
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area10800 Å2
ΔGint-136 kcal/mol
Surface area46720 Å2
MethodPISA
3
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

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)351,38916
Polymers350,6208
Non-polymers7698
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_544x+1/2,y-1/2,z-1/21
crystal symmetry operation6_564-x+1/2,-y+3/2,z-1/21
crystal symmetry operation7_654-y+3/2,x+1/2,z-1/21
crystal symmetry operation8_454y-1/2,-x+1/2,z-1/21
Buried area26620 Å2
ΔGint-283 kcal/mol
Surface area89150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.280, 123.280, 130.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a homo-tetramer which is generated by four monomers about a planar four fold axis.

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Components

#1: Protein INOSINE 5'-MONOPHOSPHATE DEHYDROGENASE


Mass: 43827.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli (E. coli) / References: UniProt: P49058, IMP dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein Solution: 0.16 mM protein, 0.5 M KCl, 50 mM Tris Cl (pH 7.5), 1 mM DTT, 10% glycerol, 1 mM IMP Well Solution: 2.2 M ammonium sulfate, PEG 550 MME, 0.1 M Tris Cl (pH 7.5), 10% ...Details: Protein Solution: 0.16 mM protein, 0.5 M KCl, 50 mM Tris Cl (pH 7.5), 1 mM DTT, 10% glycerol, 1 mM IMP Well Solution: 2.2 M ammonium sulfate, PEG 550 MME, 0.1 M Tris Cl (pH 7.5), 10% glycerol, 0.01 mM beta-mercaptoethanol IMP does not bind in crystal due to excess ammonium sulfate. Crystallization is reproducible in the absence of IMP. , VAPOR DIFFUSION, HANGING DROP, temperature 25K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.16 mMprotein1drop
20.5 M1dropKCl
350 mMTris-HCl1drop
41 mMdithiothreitol1drop
510 %glycerol1drop
61 mMIMP1drop
72.2 Mammonium sulfate1reservoir
90.1 MTris-HCl1reservoir
8PEG550 MME1reservoir
1010 %glycerol1reservoir
110.01 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 11, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 255126 / Num. obs: 36820 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 14
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.343 / Num. unique all: 3620 / % possible all: 95.8
Reflection
*PLUS
Num. measured all: 255126
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2907055.3 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3732 10.1 %RANDOM
Rwork0.214 ---
obs0.214 36820 99.6 %-
all-36820 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.48 Å2 / ksol: 0.48 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.84 Å20 Å20 Å2
2---4.84 Å20 Å2
3---9.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4564 0 10 107 4681
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 600 10 %
Rwork0.274 5428 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / % reflection Rfree: 10 % / Rfactor Rwork: 0.274

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