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- PDB-1jr1: Crystal structure of Inosine Monophosphate Dehydrogenase in compl... -

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Basic information

Entry
Database: PDB / ID: 1jr1
TitleCrystal structure of Inosine Monophosphate Dehydrogenase in complex with Mycophenolic Acid
ComponentsInosine-5'-Monophosphate Dehydrogenase 2
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / IMPD / IMPDH / GUANINE NUCLEOTIDE SYNTHESIS / MYCOPHENOLIC ACID / MPA
Function / homology
Function and homology information


'de novo' XMP biosynthetic process / lymphocyte proliferation / IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / GTP biosynthetic process / cellular response to interleukin-4 / circadian rhythm / nucleotide binding / metal ion binding ...'de novo' XMP biosynthetic process / lymphocyte proliferation / IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / GTP biosynthetic process / cellular response to interleukin-4 / circadian rhythm / nucleotide binding / metal ion binding / nucleus / cytoplasm / cytosol
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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. ...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 / 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 / : / MYCOPHENOLIC ACID / Inosine-5'-monophosphate dehydrogenase 2
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 Å
AuthorsSintchak, M.D. / Fleming, M.A. / Futer, O. / Raybuck, S.A. / Chambers, S.P. / Caron, P.R. / Murcko, M.A. / Wilson, K.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1996
Title: Structure and mechanism of inosine monophosphate dehydrogenase in complex with the immunosuppressant mycophenolic acid.
Authors: Sintchak, M.D. / Fleming, M.A. / Futer, O. / Raybuck, S.A. / Chambers, S.P. / Caron, P.R. / Murcko, M.A. / Wilson, K.P.
History
DepositionAug 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 2
B: Inosine-5'-Monophosphate Dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3378
Polymers111,9222
Non-polymers1,4156
Water3,639202
1
A: Inosine-5'-Monophosphate Dehydrogenase 2
hetero molecules

A: Inosine-5'-Monophosphate Dehydrogenase 2
hetero molecules

A: Inosine-5'-Monophosphate Dehydrogenase 2
hetero molecules

A: Inosine-5'-Monophosphate Dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,67516
Polymers223,8444
Non-polymers2,83112
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 area22920 Å2
ΔGint-92 kcal/mol
Surface area60710 Å2
MethodPISA, PQS
2
B: Inosine-5'-Monophosphate Dehydrogenase 2
hetero molecules

B: Inosine-5'-Monophosphate Dehydrogenase 2
hetero molecules

B: Inosine-5'-Monophosphate Dehydrogenase 2
hetero molecules

B: Inosine-5'-Monophosphate Dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,67516
Polymers223,8444
Non-polymers2,83112
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 area24240 Å2
ΔGint-93 kcal/mol
Surface area46850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.6, 110.6, 111.0
Angle α, β, γ (deg.)90, 90, 90
Int Tables number75
Space group name H-MP4
Detailsthe biological assembly is a tetramer generated from chain A in the asymmetric unit by the operations: -x,-y,z; -y,x,z; y,-x,z

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Components

#1: Protein Inosine-5'-Monophosphate Dehydrogenase 2 / IMP DEHYDROGENASE 2 / IMPDH-II / IMPD 2


Mass: 55961.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Production host: Escherichia coli (E. coli) / References: UniProt: P12269, IMP dehydrogenase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Chemical ChemComp-MOA / MYCOPHENOLIC ACID / 6-(1,3-DIHYDRO-7-HYDROXY-5-METHOXY-4-METHYL-1-OXOISOBENZOFURAN-6-YL)-4-METHYL-4-HEXANOIC ACID


Mass: 320.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 6000, LiCl, MES, 1-methyl-2-pyrrolidinone, 2-mercaptoethanol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
2300 mM1dropKCl
310 %glycerol1drop
42 mM1dropMPA
52 mM2-mercaptoethanol1drop
62 mMEDTA1drop
750 mMTris1drop
810 %PEG60001reservoir
91 M1reservoirLiCl
10100 mMMES1reservoir
115 %(v/v)NMP1reservoir
1240 mM2-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1995
RadiationMonochromator: Yale/MSC mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 40314 / Num. obs: 37492 / % possible obs: 93 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rsym value: 5.2
Reflection shellResolution: 2.6→2.71 Å / % possible all: 80
Reflection
*PLUS
% possible obs: 93 % / Num. measured all: 123246 / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MIR / Resolution: 2.6→8 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3617 10 %random
Rwork0.217 ---
all-38784 --
obs-36069 --
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 94 202 6296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.627
LS refinement shellResolution: 2.6→2.71 Å
RfactorNum. reflection% reflection
Rfree0.317 415 11 %
Rwork0.276 --
obs-3701 -
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.269
LS refinement shell
*PLUS
Rfactor Rfree: 0.317 / % reflection Rfree: 11 % / Rfactor Rwork: 0.276

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