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- PDB-1b3o: TERNARY COMPLEX OF HUMAN TYPE-II INOSINE MONOPHOSPHATE DEHYDROGEN... -

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Basic information

Entry
Database: PDB / ID: 1b3o
TitleTERNARY COMPLEX OF HUMAN TYPE-II INOSINE MONOPHOSPHATE DEHYDROGENASE WITH 6-CL-IMP AND SELENAZOLE ADENINE DINUCLEOTIDE
ComponentsPROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
KeywordsDEHYDROGENASE / IMPD / IMPDH / GUANINE NUCLEOTIDE SYNTHESIS
Function / homology
Function and homology information


'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / lymphocyte proliferation / IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / peroxisomal membrane / Azathioprine ADME / GTP biosynthetic process / cellular response to interleukin-4 ...'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / lymphocyte proliferation / IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / peroxisomal membrane / Azathioprine ADME / GTP biosynthetic process / cellular response to interleukin-4 / circadian rhythm / secretory granule lumen / ficolin-1-rich granule lumen / Potential therapeutics for SARS / nucleotide binding / Neutrophil degranulation / DNA binding / RNA binding / extracellular exosome / extracellular region / metal ion binding / nucleus / membrane / 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
6-CHLOROPURINE RIBOSIDE, 5'-MONOPHOSPHATE / SELENAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE / Inosine-5'-monophosphate dehydrogenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsColby, T.D. / Vanderveen, K. / Strickler, M.D. / Goldstein, B.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of human type II inosine monophosphate dehydrogenase: implications for ligand binding and drug design.
Authors: Colby, T.D. / Vanderveen, K. / Strickler, M.D. / Markham, G.D. / Goldstein, B.M.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms ...pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
B: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,91821
Polymers111,7502
Non-polymers2,16819
Water55831
1
A: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
hetero molecules

A: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
hetero molecules

A: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
hetero molecules

A: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,83512
Polymers223,4994
Non-polymers4,3368
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
2
B: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
hetero molecules

B: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
hetero molecules

B: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
hetero molecules

B: PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,83572
Polymers223,4994
Non-polymers4,33668
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
Unit cell
Length a, b, c (Å)142.260, 142.260, 174.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.371142, 0.928575, -0.001499), (0.928564, -0.371129, 0.005698), (0.004735, -0.003507, -0.999983)
Vector: -0.0626, 0.2165, -51.6926)
DetailsTHE BIOLOGICAL UNIT IS A HOMOTETRAMER. IT IS GENERATED BY A CRYSTALLOGRAPHIC FOURFOLD OPERATION ON MONOMER A (OR MONOMER B), NOT BY A SINGLE OPERATION ON BOTH.

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Components

#1: Protein PROTEIN (INOSINE MONOPHOSPHATE DEHYDROGENASE 2) / IMPD / IMPDH


Mass: 55874.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Variant: TYPE II ISOZYME / Production host: Escherichia coli (E. coli) / References: UniProt: P12268, IMP dehydrogenase
#2: Chemical ChemComp-CPR / 6-CHLOROPURINE RIBOSIDE, 5'-MONOPHOSPHATE


Mass: 367.660 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13ClN4O7P
#3: Chemical ChemComp-SAE / SELENAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE


Mass: 716.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25N7O14P2Se
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 15 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.9 Å3/Da / Density % sol: 68.93 %
Crystal growpH: 8 / Details: SEE PRIMARY REFERENCE , pH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
24-6 %PEG60001reservoir
31 M1reservoirLiCl
4100 mMTris1reservoir
55 %(v/v)methylpyrollidinone1reservoir
624 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91
DetectorType: CORNELL / Detector: CCD / Date: Aug 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. obs: 34001 / % possible obs: 86.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 10
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3 / Rsym value: 0.338 / % possible all: 56
Reflection
*PLUS
Num. measured all: 126775
Reflection shell
*PLUS
% possible obs: 56.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.853model building
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.853phasing
CNS0.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CORE DOMAIN OF IMPDH MONOMER FROM HAMSTER IMPD/IMP/MPA COMPLEX STRUCTURE

Resolution: 2.9→100 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 182886.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED MONOMER B IS THE MORE COMPLETE MONOMER IN THE ASYMMETRIC UNIT, WITH 410 OF 514 RESIDUES FITTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3199 9.6 %RANDOM
Rwork0.244 ---
obs-33236 86.4 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20 Å20 Å2
2---1.96 Å20 Å2
3---3.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.43 Å
Luzzati d res low-6 Å
Luzzati sigma a0.64 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 145 31 5536
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.731.5
X-RAY DIFFRACTIONc_mcangle_it2.962
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.413 218 10.2 %
Rwork0.404 1927 -
obs--56.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.IMPTOPOLOGY.IMPNOO
X-RAY DIFFRACTION3PARAM3.SADTOP2.SAD
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å

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