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- PDB-5upx: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

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Basic information

Entry
Database: PDB / ID: 5upx
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Listeria Monocytogenes in the presence of Xanthosine Monophosphate
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / alpha-beta structure / TIM barrel / IMPDH / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding
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
XANTHOSINE-5'-MONOPHOSPHATE / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.855 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Listeria Monocytogenes in the presence of Xanthosine Monophosphate
Authors: Kim, Y. / Makowska-Grzyska, M. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4423
Polymers40,9851
Non-polymers4572
Water2,612145
1
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,76812
Polymers163,9394
Non-polymers1,8298
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area24260 Å2
ΔGint-135 kcal/mol
Surface area54450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.148, 93.148, 95.265
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 / IMPDH


Mass: 40984.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: guaB / Plasmid: pMCSG50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q926Y9, IMP dehydrogenase
#2: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE / Xanthosine monophosphate


Mass: 365.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 12% (w/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 34028 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rsym value: 0.084 / Net I/σ(I): 15.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1648 / CC1/2: 0.74 / Rsym value: 0.768

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Processing

Software
NameVersionClassification
PHENIX(dev_2411: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJM

4mjm


Resolution: 1.855→38.597 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.87
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 1711 5.03 %random
Rwork0.1642 ---
obs0.166 34022 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.855→38.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 30 145 3002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072942
X-RAY DIFFRACTIONf_angle_d0.8493977
X-RAY DIFFRACTIONf_dihedral_angle_d19.6831769
X-RAY DIFFRACTIONf_chiral_restr0.057454
X-RAY DIFFRACTIONf_plane_restr0.005516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8548-1.90940.2971230.24442394X-RAY DIFFRACTION87
1.9094-1.9710.27011420.21562693X-RAY DIFFRACTION100
1.971-2.04150.23851200.19522736X-RAY DIFFRACTION100
2.0415-2.12320.21511450.1822730X-RAY DIFFRACTION100
2.1232-2.21980.23031610.16912687X-RAY DIFFRACTION100
2.2198-2.33680.2091520.16872720X-RAY DIFFRACTION100
2.3368-2.48320.22451430.18022678X-RAY DIFFRACTION100
2.4832-2.67490.20371440.17192746X-RAY DIFFRACTION100
2.6749-2.9440.21421610.17152697X-RAY DIFFRACTION100
2.944-3.36980.18991420.17242747X-RAY DIFFRACTION100
3.3698-4.24470.18261610.14632714X-RAY DIFFRACTION100
4.2447-38.60550.17931170.14362769X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.11720.14460.00291.9502-0.32920.7026-0.0233-0.21140.05340.06160.03140.22330.0503-0.0477-0.01740.23440.0150.03910.2417-0.02430.171427.3849-34.0916.0171
23.30470.8892-0.65664.4863-0.58462.60580.07720.30360.3841-0.2607-0.01770.7814-0.1396-0.26070.01180.2590.0466-0.06720.26130.0540.48713.5886-18.48-7.3208
31.95890.16480.46162.2791-0.29810.6104-0.03810.09360.1885-0.09360.06270.0666-0.06410.0417-0.02260.21290.00270.01810.2151-0.00140.194927.9937-25.17231.4136
43.4639-0.3176-0.19174.63790.09311.6883-0.02970.03571.0025-0.490.3082-0.8778-0.72490.58540.11420.6515-0.0611-0.00450.43770.00570.556233.4793-18.334-13.0775
51.30450.06830.10414.8181-1.88072.883-0.00540.0991-0.0486-0.53880.00950.56610.129-0.0627-0.04130.23340.0016-0.04150.2186-0.01210.30517.0069-41.9694-4.2603
63.4689-0.92060.36933.2519-0.22982.25830.11070.52720.0008-0.472-0.077-0.06040.28340.1157-0.0060.3567-0.00620.04660.27190.03880.294327.9856-47.32540.0599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 242 )
3X-RAY DIFFRACTION3chain 'A' and (resid 243 through 389 )
4X-RAY DIFFRACTION4chain 'A' and (resid 390 through 427 )
5X-RAY DIFFRACTION5chain 'A' and (resid 428 through 445 )
6X-RAY DIFFRACTION6chain 'A' and (resid 446 through 486 )

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