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

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Basic information

Entry
Database: PDB / ID: 4zqo
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with IMP and the inhibitor Q67
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOxidoreductase/Oxidoreductase inhibitor / IMPDH / delta CBS / Structural Genomics / 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 / : / S-1,2-PROPANEDIOL / Chem-Q67 / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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

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)42,6256
Polymers41,6431
Non-polymers9835
Water3,387188
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)170,50224
Polymers166,5704
Non-polymers3,93120
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 area25350 Å2
ΔGint-139 kcal/mol
Surface area45280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.252, 88.252, 84.268
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 , 6 types, 193 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-Q67 / N~2~-(2,3-dichlorophenyl)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]-L-alaninamide


Mass: 427.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16Cl2N4O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: 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
#6: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


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


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
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, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 31906 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.71 Å2 / Rsym value: 0.089 / Net I/σ(I): 10.6
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
SBC-Collectdev_1621data collection
HKL-3000data reduction
HKL-3000phasing
HKL-3000data scaling
MOLREPphasing
PHENIXdev_1621refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→30.473 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.179 1619 5.08 %random
Rwork0.153 ---
obs0.154 31901 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 1.76→30.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 64 188 2768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072752
X-RAY DIFFRACTIONf_angle_d1.1693756
X-RAY DIFFRACTIONf_dihedral_angle_d14.0581000
X-RAY DIFFRACTIONf_chiral_restr0.07445
X-RAY DIFFRACTIONf_plane_restr0.005490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.81160.24981300.23852437X-RAY DIFFRACTION97
1.8116-1.87010.23611490.20642505X-RAY DIFFRACTION100
1.8701-1.93690.1891330.17722532X-RAY DIFFRACTION100
1.9369-2.01440.20031290.16752521X-RAY DIFFRACTION100
2.0144-2.10610.18381380.1562532X-RAY DIFFRACTION100
2.1061-2.21710.18841450.14442533X-RAY DIFFRACTION100
2.2171-2.3560.19691450.1392501X-RAY DIFFRACTION100
2.356-2.53780.14661330.14422511X-RAY DIFFRACTION100
2.5378-2.7930.17391160.15042562X-RAY DIFFRACTION100
2.793-3.19680.18921140.15262542X-RAY DIFFRACTION100
3.1968-4.02620.15831590.14252529X-RAY DIFFRACTION100
4.0262-30.47770.1791280.14762577X-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)
10.649-0.52460.13461.6801-0.22320.16290.0347-0.09810.030.2033-0.0498-0.00280.02230.03290.0090.266-0.01090.00360.2582-0.01730.17537.55934.524912.2224
22.4674-0.47890.04571.75560.29020.9037-0.00540.16070.2298-0.15850.0193-0.3737-0.12340.2002-0.01280.2109-0.0420.02970.220.03880.292732.654221.769-4.7728
32.24922.1136-1.00954.712-0.64451.4638-0.0875-0.07670.02340.01690.0541-0.43770.030.22240.02220.17280.0106-0.02070.2385-0.01560.323837.583411.49836.3236
41.32720.0809-0.0852.00370.1111.019-0.02040.08010.0946-0.09910.0218-0.092-0.09370.0668-0.00090.1357-0.00370.00020.15970.00740.170122.317313.1882-0.8774
50.50830.0302-0.21271.78030.01891.08890.07440.16330.1209-0.3587-0.0328-0.2785-0.04180.0186-0.0250.2042-0.0184-0.00610.22780.02280.234819.412714.6986-9.27
62.03810.53330.97341.59270.02640.8680.01360.1949-0.0124-0.13210.0774-0.04740.0040.0735-0.0970.18950.00930.03340.2276-0.02740.21333.578417.7037-0.9656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND ( RESID 28 THROUGH 60 )A28 - 60
2X-RAY DIFFRACTION2CHAIN 'A' AND ( RESID 61 THROUGH 275 )A61 - 150
3X-RAY DIFFRACTION3CHAIN 'A' AND ( RESID 276 THROUGH 303 )A151 - 178
4X-RAY DIFFRACTION4CHAIN 'A' AND ( RESID 304 THROUGH 422 )A179 - 297
5X-RAY DIFFRACTION5CHAIN 'A' AND ( RESID 423 THROUGH 488 )A298 - 363
6X-RAY DIFFRACTION6CHAIN 'A' AND ( RESID 489 THROUGH 527 )A364 - 402

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