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- PDB-4zqm: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

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Basic information

Entry
Database: PDB / ID: 4zqm
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with XMP and NAD
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMPDH / delta-CBS / Mycobacterium tuberculosis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


XMP biosynthetic process / IMP catabolic process / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / peptidoglycan-based cell wall / nucleotide binding / metal ion binding / plasma membrane / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / XANTHOSINE-5'-MONOPHOSPHATE / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å
AuthorsKim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Kavitha, M. / Hedstrom, L. / 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 Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Plos One / Year: 2015
Title: Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds.
Authors: Makowska-Grzyska, M. / Kim, Y. / Gorla, S.K. / Wei, Y. / Mandapati, K. / Zhang, M. / Maltseva, N. / Modi, G. / Boshoff, H.I. / Gu, M. / Aldrich, C. / Cuny, G.D. / Hedstrom, L. / Joachimiak, A.
History
DepositionMay 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Feb 8, 2017Group: Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6713
Polymers41,6431
Non-polymers1,0292
Water2,900161
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)170,68512
Polymers166,5704
Non-polymers4,1158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area21350 Å2
ΔGint-121 kcal/mol
Surface area42850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.154, 88.154, 85.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
SymmetryPoint symmetry: (Schoenflies symbol: D4 (2x4 fold dihedral))

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Components

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


Mass: 41642.621 Da / Num. of mol.: 1
Fragment: UNP residues 1-125 and 253-529 linked by linker (GLY GLY)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: guaB, guaB2, Rv3411c, MTCY78.17 / Plasmid: pMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P9WKI7, IMP dehydrogenase
#2: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O9P
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.4 M Magnesium formate dyhydrate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2014
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 42708 / % possible obs: 99.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 22.64 Å2 / Rsym value: 0.075 / Net I/σ(I): 29
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.81 / % possible all: 93.1

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Processing

Software
NameVersionClassification
HKL-3000data reduction
SBC-Collectdata collection
HKL-3000phasing
HKL-3000data scaling
PHENIXdev_1839refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.602→35.802 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 2185 5.13 %
Rwork0.1604 --
obs0.1619 42579 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.8 Å2
Refinement stepCycle: LAST / Resolution: 1.602→35.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 68 161 2575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092495
X-RAY DIFFRACTIONf_angle_d1.3253409
X-RAY DIFFRACTIONf_dihedral_angle_d16.294906
X-RAY DIFFRACTIONf_chiral_restr0.051413
X-RAY DIFFRACTIONf_plane_restr0.006437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.602-1.63650.28621030.23132343X-RAY DIFFRACTION91
1.6365-1.67460.26281440.20892508X-RAY DIFFRACTION99
1.6746-1.71650.23021240.18782536X-RAY DIFFRACTION100
1.7165-1.76290.20841320.17552538X-RAY DIFFRACTION100
1.7629-1.81470.18791500.16992492X-RAY DIFFRACTION100
1.8147-1.87330.20231110.17832568X-RAY DIFFRACTION100
1.8733-1.94030.2621250.22672568X-RAY DIFFRACTION99
1.9403-2.01790.20081150.17392525X-RAY DIFFRACTION100
2.0179-2.10980.2031330.16152583X-RAY DIFFRACTION100
2.1098-2.2210.19391370.16492508X-RAY DIFFRACTION100
2.221-2.36010.21091960.17842474X-RAY DIFFRACTION99
2.3601-2.54230.19131630.16242506X-RAY DIFFRACTION100
2.5423-2.7980.19491530.16042547X-RAY DIFFRACTION100
2.798-3.20270.21851260.16182553X-RAY DIFFRACTION100
3.2027-4.03420.16911360.14712535X-RAY DIFFRACTION99
4.0342-35.81090.15151370.13572610X-RAY DIFFRACTION100
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)
10.83831.39290.38356.19150.91140.39370.01410.0627-0.015-0.341-0.007-0.13560.0043-0.0009-0.04060.21270.01640.01230.23010.00860.1515-8.00855.9805-12.193
23.77311.2805-0.20282.36930.15581.0933-0.06480.12550.4079-0.17890.02150.2702-0.19310.00790.05270.19980.0158-0.01580.18370.00340.2495-22.294927.7942-4.1236
33.41251.6592-0.09732.3357-0.10751.72370.1342-0.4190.43890.3046-0.18930.4424-0.1671-0.25720.07950.22090.0040.05990.2786-0.06950.2637-33.377521.02719.3916
43.81231.30580.53223.83780.48342.6853-0.00080.01210.2805-0.0188-0.0960.7055-0.0878-0.49990.0830.1560.0250.02660.2706-0.04450.3413-41.530416.6511.6652
52.2968-2.1132-1.1584.61770.89141.8519-0.04030.06880.0332-0.00830.04620.36550.0391-0.26080.02420.1603-0.0116-0.02140.24630.00330.2843-37.43311.4839-6.3935
61.19140.6335-0.98213.14691.05653.20350.02170.13920.0932-0.0862-0.09910.1793-0.0672-0.09920.08090.1374-0.0248-0.01510.17340.00610.1805-28.627811.9147-7.5016
71.8980.5968-0.18560.91850.54340.6424-0.05030.0140.0228-0.13930.0035-0.1666-0.0434-0.05940.11390.1612-0.0049-0.0030.1806-0.02990.1678-18.87337.1887-8.1762
82.53071.1174-0.26212.06121.05241.1640.0537-0.33-0.04380.1337-0.0075-0.09580.15350.0025-0.04310.1658-0.00020.00330.18860.010.1832-17.168917.3939-2.9063
91.86330.76550.72723.8022-0.0744.2080.006-0.98650.02090.98050.1379-0.27280.40840.2694-0.0890.47350.0232-0.04320.5058-0.05190.1999-19.979515.221419.2573
102.88650.73710.53269.10473.51124.26380.0763-0.0521-0.53060.32180.14420.0920.737-0.216-0.25290.4332-0.01330.01750.33130.00950.2418-23.83866.737513.3812
112.08390.5144-0.7942.6383-0.36372.23890.0688-0.11690.10480.1235-0.05110.0078-0.12960.0045-0.0340.1154-0.012-0.01450.14930.00450.1677-9.289822.9962-3.0409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 274 )
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 303 )
6X-RAY DIFFRACTION6chain 'A' and (resid 304 through 342 )
7X-RAY DIFFRACTION7chain 'A' and (resid 343 through 367 )
8X-RAY DIFFRACTION8chain 'A' and (resid 368 through 396 )
9X-RAY DIFFRACTION9chain 'A' and (resid 397 through 422 )
10X-RAY DIFFRACTION10chain 'A' and (resid 423 through 469 )
11X-RAY DIFFRACTION11chain 'A' and (resid 470 through 509 )

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