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

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Basic information

Entry
Database: PDB / ID: 4zqp
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with IMP and the inhibitor MAD1
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOxidoreductase/Oxidoreductase inhibitor / IMPDH / delta CBS / MAD1 / Structural Genomics / Center for Membrane Proteins of Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Oxidoreductase-Oxidoreductase inhibitor complex
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
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
INOSINIC ACID / : / Chem-KP3 / S-1,2-PROPANEDIOL / PHOSPHATE ION / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, Y. / 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 / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9027
Polymers41,6431
Non-polymers1,2596
Water3,045169
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)171,60728
Polymers166,5704
Non-polymers5,03624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area28010 Å2
ΔGint-149 kcal/mol
Surface area42780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.225, 88.225, 84.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 7 types, 175 molecules

#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-KP3 / 5'-O-({1-[(2E)-4-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)-2-methylbut-2-en-1-yl]-1H-1,2,3-triazol-4-yl}methyl)adenosine


Mass: 608.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H32N8O8
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: 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
#7: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M Na/K phosphate pH 6.2, 25 %(v/v) 1,2 propandiol, 10 %(v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2013
RadiationMonochromator: double crystal monochrimator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.9→35.76 Å / Num. obs: 25094 / % possible obs: 97 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.26 Å2 / Rsym value: 0.103 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.84 / % possible all: 78.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
HKL-3000data scaling
MOLREPphasing
PHENIXdev_1745refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.76 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1272 5.07 %random
Rwork0.143 ---
obs0.145 25083 96.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 84 169 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012716
X-RAY DIFFRACTIONf_angle_d1.383709
X-RAY DIFFRACTIONf_dihedral_angle_d14.392990
X-RAY DIFFRACTIONf_chiral_restr0.059438
X-RAY DIFFRACTIONf_plane_restr0.005480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96410.28571170.21862103X-RAY DIFFRACTION77
1.9641-2.05350.24411560.18872598X-RAY DIFFRACTION96
2.0535-2.16180.2131340.15382738X-RAY DIFFRACTION100
2.1618-2.29720.16911620.1332708X-RAY DIFFRACTION100
2.2972-2.47450.17481140.13222761X-RAY DIFFRACTION100
2.4745-2.72350.18351450.13732724X-RAY DIFFRACTION99
2.7235-3.11730.18551450.14452730X-RAY DIFFRACTION99
3.1173-3.92670.1651460.13562730X-RAY DIFFRACTION99
3.9267-35.76650.18971530.13452719X-RAY DIFFRACTION97
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)
16.3639-1.44331.98350.3742-0.47260.6090.05220.4917-0.0956-0.0714-0.0501-0.01490.01980.0981-0.01880.25390.00910.0130.25170.01360.178-44.3649-34.7787-11.8932
21.3284-0.5592-0.56392.59270.71550.8230.0378-0.05120.22420.00220.052-0.3555-0.03130.1309-0.11460.1545-0.0097-0.01440.20770.00690.2265-18.1955-22.86381.08
33.0188-1.4011-0.59633.18160.05621.5718-0.072-0.21360.54440.21410.096-0.5075-0.2420.2225-0.01470.2403-0.0355-0.03480.1912-0.03280.3265-23.8328-7.48967.7214
41.94240.63210.9562.68621.43892.86460.03940.05850.3362-0.1565-0.1039-0.1242-0.35410.00440.07230.2540.0170.02670.17130.0370.2788-31.0094-6.6527-5.4024
51.86130.0613-0.2631.46570.32910.66910.029-0.1699-0.03020.1597-0.0014-0.06560.03870.0252-0.02310.14790.0043-0.01280.13280.00850.1367-31.1323-24.4613.2519
67.9003-0.76052.07962.6528-0.68643.5688-0.0224-0.21390.09570.1970.0910.3379-0.2642-0.2421-0.0810.22540.00330.01880.1951-0.03950.1879-38.7509-19.202714.5482
72.2041-1.1535-1.78843.88353.61946.4748-0.0403-0.3066-0.04450.10510.2263-0.3776-0.03360.4541-0.19470.17290.0063-0.03260.2118-0.00240.2381-16.5919-32.31444.3573
81.80740.8509-0.0442.0783-1.02591.41140.1078-0.15330.09970.2171-0.01280.091-0.057-0.0282-0.08830.2050.02080.02760.146-0.0350.2011-26.2653-40.5581.2941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND ( RESID 28 THROUGH 52 )A28 - 52
2X-RAY DIFFRACTION2CHAIN 'A' AND ( RESID 53 THROUGH 99 )A53 - 99
3X-RAY DIFFRACTION3CHAIN 'A' AND ( RESID 100 THROUGH 262 )A100 - 137
4X-RAY DIFFRACTION4CHAIN 'A' AND ( RESID 263 THROUGH 326 )A138 - 201
5X-RAY DIFFRACTION5CHAIN 'A' AND ( RESID 327 THROUGH 422 )A202 - 297
6X-RAY DIFFRACTION6CHAIN 'A' AND ( RESID 423 THROUGH 469 )A298 - 344
7X-RAY DIFFRACTION7CHAIN 'A' AND ( RESID 470 THROUGH 487 )A345 - 362
8X-RAY DIFFRACTION8CHAIN 'A' AND ( RESID 488 THROUGH 528 )A363 - 403

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