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- PDB-7qdx: bacterial IMPDH chimera -

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Basic information

Entry
Database: PDB / ID: 7qdx
Titlebacterial IMPDH chimera
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMPDH chimera
Function / homology
Function and homology information


C-rich single-stranded DNA binding / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / guanosine tetraphosphate binding / response to UV / single-stranded DNA binding / protein homotetramerization / protein-containing complex ...C-rich single-stranded DNA binding / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / guanosine tetraphosphate binding / response to UV / single-stranded DNA binding / protein homotetramerization / protein-containing complex / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol
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-type TIM barrel
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLabesse, G. / Gelin, M. / Munier-Lehmann, H. / Gedeon, A. / Haouz, A.
Funding support France, 4items
OrganizationGrant numberCountry
Pasteur Institute France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-0005 France
Centre National de la Recherche Scientifique (CNRS) France
Institut National de la Sante et de la Recherche Medicale (INSERM) France
Citation
Journal: Protein Sci. / Year: 2023
Title: Insight into the role of the Bateman domain at the molecular and physiological levels through engineered IMP dehydrogenases.
Authors: Gedeon, A. / Ayoub, N. / Brule, S. / Raynal, B. / Karimova, G. / Gelin, M. / Mechaly, A. / Haouz, A. / Labesse, G. / Munier-Lehmann, H.
#1: Journal: Structure / Year: 2013
Title: MgATP regulates allostery and fiber formation in IMPDHs.
Authors: Labesse, G. / Munier-Lehmann, H.
History
DepositionNov 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_audit_support / struct_keywords / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id
Revision 1.2Feb 7, 2024Group: Author supporting evidence / Refinement description
Category: pdbx_audit_support / pdbx_initial_refinement_model
Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,18710
Polymers108,0612
Non-polymers2,1268
Water81145
1
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,74940
Polymers432,2458
Non-polymers8,50432
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area40230 Å2
ΔGint-292 kcal/mol
Surface area127490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.270, 109.270, 176.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 24 through 25 and (name N...
d_2ens_1(chain "B" and (resid 24 through 160 or (resid 161...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ILEILELYSLYSAA24 - 16124 - 161
d_12ASPASPGLYGLYAA166 - 235166 - 235
d_13LEULEUPROPROAA237 - 320237 - 320
d_14CYSCYSSERSERAA324 - 482324 - 482
d_21ILEILEGLYGLYBB24 - 23524 - 235
d_22LEULEUPROPROBB237 - 390237 - 390
d_23ARGARGSERSERBB445 - 482445 - 482

NCS oper: (Code: givenMatrix: (0.55994645409, 0.82851638863, 0.00453456981742), (0.828185582441, -0.559548598046, -0.0318434838299), (-0.0238455360401, 0.0215861112018, -0.999482581246)Vector: -21. ...NCS oper: (Code: given
Matrix: (0.55994645409, 0.82851638863, 0.00453456981742), (0.828185582441, -0.559548598046, -0.0318434838299), (-0.0238455360401, 0.0215861112018, -0.999482581246)
Vector: -21.3806953427, 42.1281845593, 56.7163143187)

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Components

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


Mass: 54030.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Gene: guaB, guaR, b2508, JW5401, guaB, PA3770 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0ADG7, UniProt: Q9HXM5, IMP dehydrogenase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 191 K / Method: vapor diffusion, hanging drop / Details: 10%w/v PEG 3K, 0.1 M Na Cacod 6.5 pH, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→47.05 Å / Num. obs: 53261 / % possible obs: 98.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 76.88 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.182 / Rsym value: 0.162 / Net I/av σ(I): 6.8 / Net I/σ(I): 6.8
Reflection shellResolution: 2.74→2.91 Å / Rmerge(I) obs: 0.1267 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 8420 / CC1/2: 0.445 / Rsym value: 0.1126

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dqw

4dqw


Resolution: 2.9→47.05 Å / SU ML: 0.5291 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.3255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2666 1141 5 %
Rwork0.2007 21689 -
obs0.2041 22830 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 128 45 6123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01356149
X-RAY DIFFRACTIONf_angle_d1.37258333
X-RAY DIFFRACTIONf_chiral_restr0.0668999
X-RAY DIFFRACTIONf_plane_restr0.01041061
X-RAY DIFFRACTIONf_dihedral_angle_d6.9175865
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.30668223434 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.49221410.37522689X-RAY DIFFRACTION98.88
3.03-3.190.31921420.292684X-RAY DIFFRACTION100
3.19-3.390.35061430.23822715X-RAY DIFFRACTION99.97
3.39-3.650.29511430.22742720X-RAY DIFFRACTION100
3.66-4.020.29171410.18612688X-RAY DIFFRACTION100
4.02-4.60.2161440.16032732X-RAY DIFFRACTION100
4.6-5.80.25021430.17722707X-RAY DIFFRACTION100
5.8-47.050.22431440.18752754X-RAY DIFFRACTION99.86
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)
13.00084215460.43392830189-0.1291669983252.3037136166-0.4764206754610.519107719273-0.1489042132190.301258469866-0.1004350608720.05628882248250.1716118913680.200238029578-0.108772088991-0.01861018725190.02112681550660.508585688981-0.0420257987636-0.01980414821290.4818198166030.003448888808440.50686472268922.621488492547.644904556956.6991537208
22.52721174605-0.20579126092-0.166822385852.469912168440.8273833462392.36878007106-0.1082633567480.04260576582130.471500672643-0.05239481448880.0881534479860.177530280509-0.00427964360011-0.1739929886890.09502035682030.6057909119470.01210063015010.02049277127050.69595701028-0.126195298750.83120361033-1.2040917640637.643358974736.4685972988
33.068947494940.769735636729-0.2637836115711.1285470075-0.2984692427310.8467634603090.003861250244180.1679481301340.1442768730790.05662206797280.00870553255054-0.06628752355770.10371914096-0.01135351177970.04671302918970.487196042697-1.07600658468E-5-0.01303126971910.4523824595110.04645637390510.38488598291724.504249297852.016673497961.6457204386
44.26852386332-0.901768862060.6334343958851.3807266985-0.3752578547810.3918547138870.05340734677691.087106625610.980850004993-0.242366475268-0.2752823439620.177993746032-0.0665144049153-0.265408477001-0.01719769571440.5798927853390.036381798483-0.07077414667330.6827324839570.07685485269710.52588781417440.059233940648.7627808293-10.2019970384
52.268746129941.32498445437-0.1245755732452.534240025370.1548915379792.438382571330.009813944394960.02506986532330.1212625297360.1906355170130.005573228769560.1792619044920.306584022331-0.1291478587220.02127183822330.434794616893-0.04542438025990.05033166626150.488685321787-0.05649890246550.36149216497628.578537593830.28342730722.55082928555
60.9506914728130.568771644111-1.34347327530.339959868741-0.804503572761.88881810089-0.0154471300633-0.08942176487360.2430134689090.0201757858298-0.0951878687536-0.4660519362950.229291303507-0.283962147272-0.01570522357160.626734331174-0.06813640346530.08931804789190.5903583499980.01830742855390.57280052872721.240474038816.041355643813.6151678692
71.43766293866-1.444275516550.3399119824653.067123631340.8145442577872.072302253150.1066086717550.4204359002810.0814297830949-0.3230383100640.09392603918770.08263222549240.0265394211126-0.0349741047941-0.149750091070.551212107348-0.02825726626190.08595970689420.557682648143-0.001650220971450.4582347267388.1450683734918.170310005322.2909590614
81.38252210069-0.0601383746474-1.119560892460.597859788297-0.5709414565491.542687614270.164941154956-0.07474773456150.102775302858-0.2380729028530.179191074703-0.0234271625023-0.2453390503610.511991189854-0.3001921842160.472166680994-0.04937008433230.1106885624220.5811134117390.03234170365310.35315530787414.716419080427.01224421267.50056072556
90.8076425308710.806260825861-0.3836366855531.86114528672-0.7031043526052.242930786930.1569039963530.4823801607640.5156094275660.0005783452615020.1123380227360.001353985798590.278908531739-0.06120864197880.08294426075510.543943900597-0.0252043390633-0.02554961159560.5947422676440.03399966809370.42959012242438.223548365717.1097745603-1.38521706476
101.455980098760.0756823226330.06931955477591.607860008310.3922370201071.845580558780.04200618720680.254296027859-0.1344166412110.128999896791-0.156412672813-0.2963820296250.152565794533-0.2525982054180.02190138936640.63680064357-0.03267533870040.07940483188270.448549142278-0.02235459503640.36161198622439.261839384220.6746891899-10.8114140132
113.70653674509-1.718558487620.1669131424612.38599418123-0.3537657560110.117361820115-0.1491922319030.7959815794950.516813807039-0.0380023515963-0.0142780136447-0.373371460362-0.1157767471260.5212410176170.01772088545570.697228719942-0.07369795343380.09889569310080.5789019825520.01448331620820.49109465936348.042713704936.4112767832-6.52141049717
122.92493113344-0.312397998562-0.3125662841532.72063345539-0.717073872670.682314543197-0.353304008328-0.1648393524070.5780962024790.060270903284-0.1435677300330.208112414439-0.3058153991670.02717522731550.08140360728170.603506945390.00309452171872-0.001049442522790.61346574716-0.008530005178720.35749817119235.801028732637.6037167782-4.61043103289
131.82898998453-1.168876794960.3480875985722.36135381123-0.6914973425632.824350451940.0361261635573-0.09531900501410.5524698328040.2489822118180.01910055407010.126159234676-0.570264799952-0.03566214530250.1767278190040.674537170545-0.0272529727211-0.002923906724730.556459950579-0.1177501063070.49698843818430.200927008944.0462532474-0.000585524638881
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 108 )AA24 - 1081 - 85
22chain 'A' and (resid 109 through 224 )AA109 - 22486 - 200
33chain 'A' and (resid 225 through 482 )AA225 - 482201 - 402
44chain 'B' and (resid 23 through 44 )BB23 - 441 - 22
55chain 'B' and (resid 45 through 95 )BB45 - 9523 - 73
66chain 'B' and (resid 96 through 125 )BB96 - 12574 - 103
77chain 'B' and (resid 126 through 210 )BB126 - 210104 - 184
88chain 'B' and (resid 211 through 239 )BB211 - 239185 - 213
99chain 'B' and (resid 240 through 273 )BB240 - 273214 - 247
1010chain 'B' and (resid 274 through 316 )BB274 - 316248 - 290
1111chain 'B' and (resid 317 through 346 )BB317 - 346291 - 317
1212chain 'B' and (resid 347 through 383 )BB347 - 383318 - 354
1313chain 'B' and (resid 384 through 483 )BB384 - 483355 - 403

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