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- PDB-1nfb: Ternary complex of the human type II Inosine Monophosphate Dedhyd... -

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Basic information

Entry
Database: PDB / ID: 1nfb
TitleTernary complex of the human type II Inosine Monophosphate Dedhydrogenase with 6Cl-IMP and NAD
ComponentsInosine-5'-monophosphate dehydrogenase 2
KeywordsOXIDOREDUCTASE / 8 STRANDED PARALLE ALPHA/BETA BARREL / DEHYDROGENASE / IMPD / IMPDH / GUANINE NUCLEOTIDE BIOSYNTHESIS NAD
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Inosine-5'-monophosphate dehydrogenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRisal, D. / Strickler, M.D. / Goldstein, B.M.
CitationJournal: To be Published
Title: The Conformation of NAD Bound to Human Inosine Monophosphate Dehydrogenase Type II
Authors: Risal, D. / Strickler, M.D. / Goldstein, B.M.
History
DepositionDec 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: 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_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 1.4Dec 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: Inosine-5'-monophosphate dehydrogenase 2
B: Inosine-5'-monophosphate dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8126
Polymers111,7502
Non-polymers2,0624
Water1,56787
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)227,62412
Polymers223,4994
Non-polymers4,1248
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 area18810 Å2
ΔGint-100 kcal/mol
Surface area66410 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)227,62412
Polymers223,4994
Non-polymers4,1248
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 area18830 Å2
ΔGint-106 kcal/mol
Surface area66130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)145.190, 145.190, 127.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Inosine-5'-monophosphate dehydrogenase 2 / IMP dehydrogenase 2 / IMPDH-II / IMPD 2


Mass: 55874.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IMPDH2 / Plasmid: pET12B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.06 Å3/Da / Density % sol: 69.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% PEG 6000, 0.1M Tris-HCl, 24mM beta-mercaptoethanol, 1M LiCl, 20% Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2002 / Details: mirrors
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.9→51.33 Å / Num. all: 29280 / Num. obs: 24775 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 17.37
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1757 / Rsym value: 0.343 / % possible all: 81

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain A of PDB ENTRY 1B3O

1b3o


Resolution: 2.9→47.82 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1964 10.1 %RANDOM
Rwork0.229 ---
all0.291 29280 --
obs0.229 19483 66.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.7494 Å2 / ksol: 0.344832 e/Å3
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.78 Å20 Å20 Å2
2---4.78 Å20 Å2
3---9.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-51.3 Å
Luzzati sigma a0.53 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 132 87 5885
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it5.621.5
X-RAY DIFFRACTIONc_mcangle_it9.712
X-RAY DIFFRACTIONc_scbond_it8.142
X-RAY DIFFRACTIONc_scangle_it12.72.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 187 10.7 %
Rwork0.334 1567 -
obs-1567 36.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_6CL_AUTO_REP_MET_PRODRG.PARAMPROTEIN_6CL_AUTO_PRODRG.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMNAD_ADH_TRP_PRODRG.TOP
X-RAY DIFFRACTION3NAD.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.TOP

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