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- PDB-4xwu: Structure of the IMP dehydrogenase from Ashbya gossypii -

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Basic information

Entry
Database: PDB / ID: 4xwu
TitleStructure of the IMP dehydrogenase from Ashbya gossypii
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMP dehydrogenase / Ashbya gossypii
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...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 / CBS domain superfamily / 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
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesAshbya gossypii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBuey, R.M. / Ledesma-Amaro, R. / Balsera, M. / de Pereda, J.M. / Revuelta, J.L.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Increased riboflavin production by manipulation of inosine 5'-monophosphate dehydrogenase in Ashbya gossypii.
Authors: Buey, R.M. / Ledesma-Amaro, R. / Balsera, M. / de Pereda, J.M. / Revuelta, J.L.
History
DepositionJan 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)44,5291
Polymers44,5291
Non-polymers00
Water1,71195
1
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

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

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

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


Theoretical massNumber of molelcules
Total (without water)178,1144
Polymers178,1144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area12160 Å2
ΔGint-71 kcal/mol
Surface area42920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.787, 106.787, 69.681
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,Inosine-5'-monophosphate dehydrogenase / IMPDH


Mass: 44528.555 Da / Num. of mol.: 1 / Fragment: UNP residues 1-119,UNP residues 236-522
Mutation: The CBS domain (residues 120-325) has been replaced by the sequence stretch SQDG. Residues numbered according to the full-length wild-type sequence,The CBS domain (residues 120-325) has ...Mutation: The CBS domain (residues 120-325) has been replaced by the sequence stretch SQDG. Residues numbered according to the full-length wild-type sequence,The CBS domain (residues 120-325) has been replaced by the sequence stretch SQDG. Residues numbered according to the full-length wild-type sequence
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 (E. coli) / References: UniProt: Q756Z6, IMP dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 40% PEG-300, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→39.39 Å / Num. obs: 39565 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.0397 / Net I/σ(I): 30.28
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 1.88 / % possible all: 100

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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: 4avf
Resolution: 1.75→39.39 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 1946 4.92 %
Rwork0.167 --
obs0.1683 39552 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 0 95 2359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062299
X-RAY DIFFRACTIONf_angle_d0.953116
X-RAY DIFFRACTIONf_dihedral_angle_d11.566803
X-RAY DIFFRACTIONf_chiral_restr0.034372
X-RAY DIFFRACTIONf_plane_restr0.004403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.79380.33871400.34912670X-RAY DIFFRACTION100
1.7938-1.84230.30431640.27852686X-RAY DIFFRACTION100
1.8423-1.89650.22431150.22232679X-RAY DIFFRACTION100
1.8965-1.95770.26321570.22042635X-RAY DIFFRACTION100
1.9577-2.02770.21331290.17462694X-RAY DIFFRACTION100
2.0277-2.10890.19821490.17422643X-RAY DIFFRACTION100
2.1089-2.20490.21231290.15552679X-RAY DIFFRACTION100
2.2049-2.32110.21511220.15862723X-RAY DIFFRACTION100
2.3211-2.46650.16681400.14712667X-RAY DIFFRACTION100
2.4665-2.65690.1961340.16322682X-RAY DIFFRACTION100
2.6569-2.92420.17161640.16582674X-RAY DIFFRACTION100
2.9242-3.34710.1961410.17392692X-RAY DIFFRACTION100
3.3471-4.21630.18461210.15652717X-RAY DIFFRACTION100
4.2163-39.40270.18161410.16182765X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.06971.2069-0.38520.9955-0.25980.85510.0609-0.13260.38950.01130.0780.0221-0.1669-0.1455-0.00010.34690.07530.03790.3499-0.00530.290899.8589128.695814.2783
21.17410.28280.43750.09250.1130.1726-0.31051.38520.2427-0.92630.44210.3220.2223-0.75130.06270.6467-0.06480.14150.66640.20040.4928118.2695140.8435-8.1094
30.62710.28830.50960.2330.0950.5228-0.24030.60860.5029-0.51530.305-0.2274-0.2094-0.0598-0.00980.6517-0.06570.20530.5130.16660.5372125.8622144.772-7.0027
41.45571.4545-0.92291.7561-0.54952.51850.17080.06420.4952-0.2142-0.1056-0.2748-0.29470.11550.00030.4162-0.07830.1060.32250.0510.5487129.3927142.35073.3985
53.16150.4333-0.37312.5656-0.42621.68440.12490.15420.29780.050.0384-0.0767-0.18350.06790.00020.3456-0.02410.04510.2759-0.00880.2718118.7495131.321310.2819
60.0550.0082-0.02990.0329-0.02360.0389-0.23431.4440.044-0.27020.55720.4950.1983-0.58610.00010.6978-0.1357-0.01190.82580.14560.4446112.4286136.0277-12.2795
72.52010.9434-0.70731.025-0.54960.6041-0.05560.4590.5701-0.22430.18950.36510.0262-0.3495-0.00360.39780.01240.01070.41140.08770.4146101.2219133.54267.8329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 296 )
5X-RAY DIFFRACTION5chain 'A' and (resid 297 through 389 )
6X-RAY DIFFRACTION6chain 'A' and (resid 390 through 459 )
7X-RAY DIFFRACTION7chain 'A' and (resid 460 through 500 )

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