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- PDB-4z0g: Structure of the IMPDH from Ashbya gossypii bound to GMP -

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Basic information

Entry
Database: PDB / ID: 4z0g
TitleStructure of the IMPDH from Ashbya gossypii bound to GMP
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
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 / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS 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 / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / 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
GUANOSINE-5'-MONOPHOSPHATE / : / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesAshbya gossypii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBuey, R.M. / de Pereda, J.M. / Revuelta, J.L.
CitationJournal: Nat Commun / Year: 2015
Title: Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases.
Authors: Buey, R.M. / Ledesma-Amaro, R. / Velazquez-Campoy, A. / Balsera, M. / Chagoyen, M. / de Pereda, J.M. / Revuelta, J.L.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,77210
Polymers89,0572
Non-polymers1,7158
Water11,620645
1
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,54520
Polymers178,1144
Non-polymers3,43116
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 area28560 Å2
ΔGint-147 kcal/mol
Surface area50420 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,54520
Polymers178,1144
Non-polymers3,43116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area28850 Å2
ΔGint-144 kcal/mol
Surface area51440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.480, 117.480, 56.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11B-1023-

HOH

21B-1024-

HOH

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Components

#1: Protein Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase / IMPDH


Mass: 44528.555 Da / Num. of mol.: 2 / Fragment: UNP residues 1-119,UNP residues 236-522
Mutation: The whole Bateman domain (residues 116-235) has been replaced by the sequence stretch "SQDG"
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus)
Gene: AGOS_AER117W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q756Z6, IMP dehydrogenase
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% (v/v) 1,2-propanediol 5% (w/v) PEG-3000 10% (v/v) glycerol 0.1 M Natrium phosphate-citrate, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.25→56.53 Å / Num. obs: 212581 / % possible obs: 99.9 % / Redundancy: 12.93 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.88
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 9.95 % / Rmerge(I) obs: 1.61 / Mean I/σ(I) obs: 1.54 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XWU

4xwu


Resolution: 1.25→56.525 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1482 10645 5.01 %
Rwork0.1241 --
obs0.1252 212410 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→56.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 110 645 6536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115999
X-RAY DIFFRACTIONf_angle_d1.3418117
X-RAY DIFFRACTIONf_dihedral_angle_d12.0622163
X-RAY DIFFRACTIONf_chiral_restr0.081939
X-RAY DIFFRACTIONf_plane_restr0.0071030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2501-1.26430.35273400.34646549X-RAY DIFFRACTION98
1.2643-1.27910.30253440.30626665X-RAY DIFFRACTION100
1.2791-1.29470.29573810.28046643X-RAY DIFFRACTION100
1.2947-1.31110.27643750.25646714X-RAY DIFFRACTION100
1.3111-1.32840.27473480.23046680X-RAY DIFFRACTION100
1.3284-1.34660.23813970.21536665X-RAY DIFFRACTION100
1.3466-1.36580.20553780.19226669X-RAY DIFFRACTION100
1.3658-1.38620.20513240.1736746X-RAY DIFFRACTION100
1.3862-1.40790.20383720.16056681X-RAY DIFFRACTION100
1.4079-1.4310.17373390.14086728X-RAY DIFFRACTION100
1.431-1.45560.16523500.13046728X-RAY DIFFRACTION100
1.4556-1.48210.17423660.12256699X-RAY DIFFRACTION100
1.4821-1.51060.15753440.11216750X-RAY DIFFRACTION100
1.5106-1.54150.15333630.10676664X-RAY DIFFRACTION100
1.5415-1.5750.14533500.10136681X-RAY DIFFRACTION100
1.575-1.61160.14293100.10256836X-RAY DIFFRACTION100
1.6116-1.65190.12913770.08746613X-RAY DIFFRACTION100
1.6519-1.69660.12013560.08556715X-RAY DIFFRACTION100
1.6966-1.74650.11773570.08686735X-RAY DIFFRACTION100
1.7465-1.80290.12653660.08346703X-RAY DIFFRACTION100
1.8029-1.86730.12383850.09096719X-RAY DIFFRACTION100
1.8673-1.94210.12873500.09086730X-RAY DIFFRACTION100
1.9421-2.03050.12323750.0956747X-RAY DIFFRACTION100
2.0305-2.13750.12713490.09816751X-RAY DIFFRACTION100
2.1375-2.27150.11933360.09826748X-RAY DIFFRACTION100
2.2715-2.44690.12653520.10226771X-RAY DIFFRACTION100
2.4469-2.69310.12863270.11156777X-RAY DIFFRACTION100
2.6931-3.08280.14773200.1266865X-RAY DIFFRACTION100
3.0828-3.88380.14433860.12766777X-RAY DIFFRACTION100
3.8838-56.58280.15653280.14757016X-RAY DIFFRACTION100

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