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- PDB-1jcn: BINARY COMPLEX OF HUMAN TYPE-I INOSINE MONOPHOSPHATE DEHYDROGENAS... -

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Basic information

Entry
Database: PDB / ID: 1jcn
TitleBINARY COMPLEX OF HUMAN TYPE-I INOSINE MONOPHOSPHATE DEHYDROGENASE WITH 6-CL-IMP
ComponentsINOSINE MONOPHOSPHATE DEHYDROGENASE I
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / IMPD / IMPDH / GUANINE NUCLEOTIDE SYNTHESIS
Function / homology
Function and homology information


Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / azurophil granule lumen / secretory granule lumen / ficolin-1-rich granule lumen / Potential therapeutics for SARS ...Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / azurophil granule lumen / secretory granule lumen / ficolin-1-rich granule lumen / Potential therapeutics for SARS / nucleic acid binding / nucleotide binding / Neutrophil degranulation / DNA binding / RNA binding / extracellular region / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. ...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 / 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 / Inosine-5'-monophosphate dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRisal, D. / Strickler, M.D. / Goldstein, B.M.
CitationJournal: To be Published
Title: Crystal Structure of the Human Type I Inosine Monophosphate Dehydrogenase and Implications for Isoform Specificity
Authors: Risal, D. / Strickler, M.D. / Goldstein, B.M.
History
DepositionJun 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: 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 1.4Apr 3, 2024Group: 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_conn / struct_sheet / 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_sheet.number_strands / _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 MONOPHOSPHATE DEHYDROGENASE I
B: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7634
Polymers111,0272
Non-polymers7352
Water5,296294
1
A: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules

A: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules

A: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules

A: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,5258
Polymers222,0544
Non-polymers1,4714
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
Buried area13960 Å2
ΔGint-109 kcal/mol
Surface area65540 Å2
MethodPISA, PQS
2
B: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules

B: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules

B: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules

B: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,5258
Polymers222,0544
Non-polymers1,4714
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
Buried area14250 Å2
ΔGint-107 kcal/mol
Surface area66190 Å2
MethodPISA, PQS
3
A: INOSINE MONOPHOSPHATE DEHYDROGENASE I
B: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules

A: INOSINE MONOPHOSPHATE DEHYDROGENASE I
B: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules

A: INOSINE MONOPHOSPHATE DEHYDROGENASE I
B: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules

A: INOSINE MONOPHOSPHATE DEHYDROGENASE I
B: INOSINE MONOPHOSPHATE DEHYDROGENASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)447,05016
Polymers444,1098
Non-polymers2,9418
Water1448
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
Buried area37060 Å2
ΔGint-212 kcal/mol
Surface area122870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.108, 148.108, 122.016
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: (-0.00014, 1, -0.00042), (1, 0.00014, -2.0E-5), (-2.0E-5, -0.00042, -1)
Vector: 0.02299, -0.00456, 56.07062)

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Components

#1: Protein INOSINE MONOPHOSPHATE DEHYDROGENASE I / IMPD / IMPDH / INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 1


Mass: 55513.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: impdh1 / Variant: TYPE I ISOZYME / Plasmid: pIMP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20839, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 3 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PROTEIN SOLUTION: 7MGS/ML PROTEIN, 50 MM TRIS HCL (PH 8.0), 50 MM KCL, 2MM EDTA, 1MM DTT, 5MM 6-CL-IMP. WELL SOLUTION: 9% (W/V) PEG-800, 100 MM TRIS HCL (PH 8.0), 1.0 M LICL, 24 MM ...Details: PROTEIN SOLUTION: 7MGS/ML PROTEIN, 50 MM TRIS HCL (PH 8.0), 50 MM KCL, 2MM EDTA, 1MM DTT, 5MM 6-CL-IMP. WELL SOLUTION: 9% (W/V) PEG-800, 100 MM TRIS HCL (PH 8.0), 1.0 M LICL, 24 MM BETAMERCAPTOETHANOL (2+2 MICROLITER DROPS), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→39.74 Å / Num. all: 44411 / Num. obs: 44411 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.366 / % possible all: 93.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
DPSdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CORE DOMAIN OF IMPDH MONOMER FROM HUMAN TYPE II/6-CL-IMP COMPLEX STRUCTURE

Resolution: 2.5→39.74 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2983561.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Details: 45 RESIDUES OF THE FLANKING DOMAIN AND 50 RESIDUES OF THE ACTIVE-SITE FLAP ARE DISORDERED IN BOTH MONOMERS. 6 RESIDUES IN THE FLANKING DOMAIN HAVE BEEN MODELLED UP TO THE CB DUE TO LACK OF ...Details: 45 RESIDUES OF THE FLANKING DOMAIN AND 50 RESIDUES OF THE ACTIVE-SITE FLAP ARE DISORDERED IN BOTH MONOMERS. 6 RESIDUES IN THE FLANKING DOMAIN HAVE BEEN MODELLED UP TO THE CB DUE TO LACK OF ROBUST SIDE-CHAIN ELECTRON DENSITY. SEGMENTS OF THE CORE DOMAIN RELATED BY NCS-SYMMETRY HAD NCS RESTRAINTS ON BACKBONE C-ALPHA, N, AND C ATOMS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 4483 10.1 %RANDOM
Rwork0.238 ---
all0.238 44410 --
obs0.238 44410 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.48 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-6 Å
Luzzati sigma a0.24 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 44 294 6216
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 723 10.2 %
Rwork0.266 6364 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_IMP_AUTO_REP.PARAMPROTEIN_IMP_AUTO.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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