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- PDB-1zfj: INOSINE MONOPHOSPHATE DEHYDROGENASE (IMPDH; EC 1.1.1.205) FROM ST... -

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Basic information

Entry
Database: PDB / ID: 1zfj
TitleINOSINE MONOPHOSPHATE DEHYDROGENASE (IMPDH; EC 1.1.1.205) FROM STREPTOCOCCUS PYOGENES
ComponentsINOSINE MONOPHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / IMPDH / DEHYDROGENASE / CBS DOMAINS
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / 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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I ...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
INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsZhang, R. / Evans, G. / Rotella, F.J. / Westbrook, E.M. / Beno, D. / Huberman, E. / Joachimiak, A. / Collart, F.R.
CitationJournal: Biochemistry / Year: 1999
Title: Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase.
Authors: Zhang, R. / Evans, G. / Rotella, F.J. / Westbrook, E.M. / Beno, D. / Huberman, E. / Joachimiak, A. / Collart, F.R.
History
DepositionMar 29, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_ref_seq_dif / 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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5772
Polymers53,2281
Non-polymers3481
Water8,989499
1
A: INOSINE MONOPHOSPHATE DEHYDROGENASE
hetero molecules

A: INOSINE MONOPHOSPHATE DEHYDROGENASE
hetero molecules

A: INOSINE MONOPHOSPHATE DEHYDROGENASE
hetero molecules

A: INOSINE MONOPHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,3068
Polymers212,9134
Non-polymers1,3934
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 area21490 Å2
ΔGint-121 kcal/mol
Surface area72650 Å2
MethodPISA
2
A: INOSINE MONOPHOSPHATE DEHYDROGENASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)428,61216
Polymers425,8278
Non-polymers2,7868
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_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area54690 Å2
ΔGint-237 kcal/mol
Surface area133580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.480, 151.480, 101.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsS. PYOGENES IMPDH IS A TETRAMER WITH ITS FOUR SUBUNITS RELATED BY A CRYSTALLOGRAPHIC FOURFOLD AXIS. EACH MONOMER HAS A TWO-DOMAIN STRUCTURE: A CATALYTIC DOMAIN (AMINO ACID RESIDUES 2-92 AND 224-492) FORMING THE INTERIOR CORE OF THE ACTIVE TETRAMERIC ENZYME AND A CBS DIMER DOMAIN (RESIDUES 93-223) PROJECTING OUTWARD FROM THE CORNERS OF THE SQUARE. THE CBS DESIGNATION ARISES FROM THE ORIGINAL IDENTIFICATION OF THIS FOLDING MOTIF IN THE ENZYME CYSTATHIONINE-"BETA"-SYNTHASE [BATEMAN, A. (1997) TRENDS BIOCHEM. SCI. 22, 12-13]. THE CBS DIMER DOMAIN, FOUND IN IMPDH PROTEINS FROM ALL THREE KINGDOMS, IS COMPOSED OF TWO CBS MOTIFS RELATED BY APPROXIMATE TWOFOLD SYMMETRY (RMS DEVIATIONS BETWEEN ALPHA CARBON ATOMS: 2.7 ANGSTROMS). EACH CBS MOTIF HAS THE CHARACTERISTIC SHEET/HELIX/SHEET/SHEET/HELIX TOPOLOGY. THIS IS THE FIRST REPORTED COMPLETE STRUCTURE OF A CBS DIMER DOMAIN, A FOLDING MOTIF PROPOSED TO ACT AS A REGULATORY ELEMENT SINCE MUTATIONS LEAD TO THE HUMAN DISEASE HOMOCYSTINURIA. EACH IPMDH MONOMER CONTAINS IMP IN THE CATALYTIC SITE. THIS SUBSTRATE IS NOT COVALENTLY BOUND TO THE ACTIVE SITE CYS310 SUGGESTING THAT IMP DOES NOT FORM A COVALENT BOND IN THE ABSENCE OF NAD.

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Components

#1: Protein INOSINE MONOPHOSPHATE DEHYDROGENASE


Mass: 53228.352 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, CBS DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Streptococcus pyogenes (bacteria) / Strain (production host): ESCHERICHIA COLI / References: UniProt: P0C0H6, IMP dehydrogenase
#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.74 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.2
Details: 0.1 M MES (PH 7.2), 1.8 M AMMONIUM SULFATE, 10 MM COCL2, pH 7.20
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MMES1reservoir
21.8 Mammonium sulfate1reservoir
310 mM1reservoirCoCl2
420 mg/mlprotein1drop
510 mMBis-Tris-propane1drop
61 mMIMP1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791,1.0781
DetectorType: SBC-1 / Detector: CCD / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
21.07811
ReflectionResolution: 1.9→40 Å / Num. obs: 44921 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.5 / % possible all: 87.6
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40 Å / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Num. measured all: 263355
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
CNSrefinement
CCP4model building
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
CNSphasing
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 986591.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3980 10 %RANDOM
Rwork0.232 ---
obs-39729 88.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.84 Å20 Å20 Å2
2--9.84 Å20 Å2
3----19.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 23 499 4066
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
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_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 1.9→2.01 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 534 10.2 %
Rwork0.357 4706 -
obs--70.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3IMP.PARIMP.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.37
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / Rfactor Rwork: 0.357

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