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- PDB-7qem: bacterial IMPDH chimera -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7qem
Titlebacterial IMPDH chimera
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Nucleotide synthesis
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 / 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
INOSINIC ACID / 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: 3.09 Å
AuthorsLabesse, G. / Gelin, M. / Gedeon, A. / Haouz, A. / Munier-Lehmann, H.
Funding support France, 4items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-0005 France
Pasteur Institute 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. / Alexandre, T. / Vaupre, L. / Salard-Arnaud, I. / Him, J.L. / Raynal, B. / Bron, P. / Munier-Lehmann, H.
History
DepositionDec 3, 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
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,5158
Polymers216,1224
Non-polymers1,3934
Water30617
1
A: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)435,03116
Polymers432,2458
Non-polymers2,7868
Water1448
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
2
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)435,03116
Polymers432,2458
Non-polymers2,7868
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
Unit cell
Length a, b, c (Å)143.320, 143.320, 119.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Space group name HallP4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 83 or resid 85...
d_2ens_1(chain "B" and (resid 2 through 83 or resid 85...
d_3ens_1(chain "D" and (resid 2 through 83 or resid 85...

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_11LEULEUVALVALAA2 - 8322 - 103
d_12ARGARGPROPROAA85 - 300105 - 320
d_13CYSCYSTYRTYRAA304 - 376324 - 396
d_14ARGARGSERSERAA379 - 383399 - 403
d_15VALVALGLYGLYAA420 - 463440 - 483
d_21LEULEUVALVALBB2 - 8322 - 103
d_22ARGARGPROPROBB85 - 142105 - 162
d_23ASPASPPROPROBB146 - 300166 - 320
d_24CYSCYSGLYGLYBB304 - 463324 - 483
d_31LEULEUVALVALDD2 - 8322 - 103
d_32ARGARGPROPRODD85 - 142105 - 162
d_33ASPASPTYRTYRDD146 - 376166 - 396
d_34ARGARGSERSERDD379 - 383399 - 403
d_35VALVALGLYGLYDD420 - 463440 - 483

NCS oper:
IDCodeMatrixVector
1given(0.524650293548, 0.851312564853, 0.00299773319751), (0.850950267001, -0.524523978409, 0.0275361428795), (0.0250142473639, -0.0118959235801, -0.999616313608)24.4570622933, -97.4963122077, -15.0493517233
2given(-0.209964249497, -0.977627753107, 0.0126091351136), (-0.976854497626, 0.209224190749, -0.044503128803), (0.0408693577277, -0.0216613563863, -0.998929667814)16.3944128445, 12.1221066452, -77.5845132227

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Components

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


Mass: 54030.613 Da / Num. of mol.: 4
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-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1%w/v Tryptone, 0.05 M HEPES 7 pH, 12%w/v PEG 3350, 0.001% w/V NaN3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.07→47.77 Å / Num. obs: 44463 / % possible obs: 98 % / Redundancy: 13.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.415 / Rpim(I) all: 0.119 / Rrim(I) all: 0.432 / Χ2: 1.2 / Net I/σ(I): 6
Reflection shellResolution: 3.07→3.15 Å / Redundancy: 11.2 % / Rmerge(I) obs: 2.788 / Mean I/σ(I) obs: 1 / Num. unique obs: 2450 / CC1/2: 0.314 / Rpim(I) all: 0.832 / Rrim(I) all: 2.914 / Χ2: 1.03 / % possible all: 73.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DQW

4dqw


Resolution: 3.09→47.77 Å / Cross valid method: FREE R-VALUE / σ(F): 560.92 / Phase error: 32.7564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2412 2003 4.52 %
Rwork0.1991 42276 -
obs0.2029 44279 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.99 Å2
Refinement stepCycle: LAST / Resolution: 3.09→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12036 0 83 17 12136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010812264
X-RAY DIFFRACTIONf_angle_d1.29616556
X-RAY DIFFRACTIONf_chiral_restr0.06321975
X-RAY DIFFRACTIONf_plane_restr0.01212136
X-RAY DIFFRACTIONf_dihedral_angle_d8.15621786
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.53141267729
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.38719222764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.170.38571390.2942921X-RAY DIFFRACTION91.6
3.17-3.250.33561410.27922996X-RAY DIFFRACTION95.47
3.25-3.350.31071380.27283018X-RAY DIFFRACTION95.63
3.35-3.460.37211430.25763003X-RAY DIFFRACTION95.45
3.46-3.580.34661420.24033019X-RAY DIFFRACTION95.51
3.58-3.720.25571410.23283020X-RAY DIFFRACTION95.54
3.72-3.890.25861440.20833005X-RAY DIFFRACTION95.43
3.89-4.10.21551400.19653028X-RAY DIFFRACTION95.58
4.1-4.350.22081450.18393016X-RAY DIFFRACTION95.41
4.35-4.690.21461450.16933021X-RAY DIFFRACTION95.42
4.69-5.160.18461440.17283032X-RAY DIFFRACTION95.47
5.16-5.910.23861440.19543031X-RAY DIFFRACTION95.46
5.91-7.440.21331410.18623066X-RAY DIFFRACTION95.6
7.44-47.770.21361520.173104X-RAY DIFFRACTION95.33
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)
11.58031967325-0.8088461852010.3032685856281.5239134643-0.9630328473120.9139797136770.02051299240770.2080998648180.0426491535008-0.186870893361-0.06043027930890.01152904357210.1199355263660.06302266292220.04939894023820.4769828769620.0161414877055-0.04173563941420.390801807044-0.08398949696210.89032180078455.3325647658-39.0395858288-17.5701891002
24.955412910142.368137492851.93596192935.329844817351.524816426372.04895936233-0.2746860269730.6345090580450.493343181936-0.484204486230.102583587607-0.162411834618-1.013119733430.7504969404860.2200131117280.6857658770780.1465819513850.1045863216780.7965480213030.04114039282420.95016211041542.0029789453-12.3326040301-44.1713616493
35.571066353483.03243350996-0.2368687087823.90512999767-1.031917048099.07317581648-0.05199563676630.1356086911080.5850729515350.039852411469-0.001638701896340.204783925262-0.7710071956080.04404608944470.05519921910760.6511902870810.0350161321526-0.1263049248650.504261983959-0.05920685281020.94553268347837.3272619023-14.6108976726-30.4176057935
43.49658357509-2.38838762595-0.6270438605713.62351349576-1.575565364752.01235998935-0.0615952910311-0.03043291673531.12745232259-0.101814456572-0.026529240615-0.390214801962-0.476183876040.158140849960.1223950786160.553923614820.0131450450924-0.05045040739410.352242193592-0.06234455747061.0439982270362.4081945328-31.1307118971-11.6259479323
56.2145480081.641117521062.063204131773.78325862576-0.978129057192.242161975550.0986980996636-0.141497436192-0.182033188279-0.243447830066-0.0942746344235-0.2049906739730.04284815401140.2786328460.06867342003970.3567184147880.0348529846888-0.02066088581090.4283407476760.06881610071160.77754876647366.8657857619-45.4244594388-5.84380367738
63.172181795161.34499456501-0.3290288237165.44269425286-2.743588793862.66488401815-0.09911062080290.536015597614-0.231493717902-0.582280048243-0.00567071021484-0.005866661667660.435820753582-0.05668539586910.05202160211260.396941032150.0163069226545-0.03724955104810.493609495293-0.1510041543870.95059313037155.1859321158-51.9061444605-19.1026488073
72.73392119898-1.303081078290.2552292005012.84880455305-0.2226760684411.52683395245-0.230757359746-0.310437358439-0.3019959919810.425786595860.123037509764-0.2313458217830.148296925150.3792436382580.1014507907390.492256893550.0681089168333-0.01886030041270.5546800150410.05213968033080.63414570540818.7068649652-27.19666355662.73056074353
82.479539779-2.926545248622.597553864254.38113330398-3.678390584565.993781109090.509159174235-0.295821228111-0.2168879202170.679640480882-0.0129705731649-0.0758508147805-0.431914407685-0.750283002655-0.5081307436361.149279303780.0176969487406-0.3829768017071.02588060310.2286745933651.2104898164637.4387337246-55.714059824230.3224597318
99.530465551593.52990860796-0.2410051343513.66456414813.356035169744.94646605382-0.0208850207795-0.0267587177029-0.5657058836480.0630545622716-0.46783722366-1.031554392130.8086335290980.651545788390.511653428590.9298191592670.267276891612-0.03679839533730.7339416547080.2417261477321.2551357879136.8685586844-63.063995605321.9887422158
100.171923867768-0.9771085130410.5859802591312.90414417946-1.712519762210.943478774171-0.0444157594261-0.1717791544970.1465254559220.625468646423-0.277674451281-0.4674660019270.2052270744950.03935810520840.1890651603340.954251654857-0.0891503054616-0.1078290201140.7974483855530.1888818351981.2072726330624.138653218-53.710497338312.4013989289
112.479376528830.787564965356-0.6950205759022.8702621807-0.5094807863421.90350729505-0.0605639873189-0.316453177844-0.05205160915450.1342008314490.0670960761735-0.0829246264249-0.03634218589290.169662563473-0.0270714872970.3855587957280.0522414443328-0.005653549001170.447978660175-0.002664941761650.7208391093719.3370889219-22.0629383334-0.195640581948
122.16375517367-0.568307957264-0.3577223755292.378888756780.9179042668291.23890872483-0.2108490530560.517434737365-0.457280947186-0.2396955845480.1366830768260.05042643816330.0797427542589-0.109313276393-0.008102359554110.551782008919-0.1158291552490.06368569835070.505868004395-0.04113671094760.711772539384.74769562938-35.300155978843.8560307152
131.72193432056-2.71805675763-2.969345800837.406369299914.43131946054.55564067564-0.3763361638080.128905779887-0.5442639515880.298055496491-0.283361722056-0.261558868681-0.0374930102491-0.7666897785650.6820741325620.600325037618-0.135658414578-0.01118409335910.685695207829-0.03478066737021.0043332935117.8403234939-55.457016154439.6058863428
141.5102896612-2.324524342520.07382593854634.666332665161.220508238771.914041256760.08721789268620.469353463432-0.404629146406-0.481345983848-0.1579387437410.646856497590.477913362377-0.540575371676-0.03334758173550.636390591487-0.154120707779-0.00995028394820.565709174657-0.027970934850.751859121861-10.9935413808-39.960861210651.1771908006
152.63696566809-1.203582750150.3249630420012.964958252211.787014286911.64254665723-0.139330475414-0.162926719276-0.175759649196-0.5162893312930.19816440337-0.4863615538020.1019648286370.004258124912220.03776938890990.563347644291-0.0318964371-0.02214769839220.404756085804-0.06430444441470.778884422379-6.18441651694-26.759658953156.1116100393
166.42402323831.84075146926-0.9411037504982.63600128997-0.6995658856782.92541677729-0.2159228717490.6586121478980.217466690213-0.4576215835340.1758064272920.06417777142890.1633712449440.02436849399230.1348841266710.4487890299740.016418467598-0.06662250420530.389544650092-0.05123101538360.6981462598428.15300150774-24.471861669744.5386485689
172.08555253867-2.64685356867-1.568051315062.053984669170.8064913284931.0030901275-0.05846860924680.208131744436-0.08060726049640.297401480205-0.2259128541190.2662022781060.0440078382542-0.1909283250770.3143702192470.6272486662070.0333738293272-0.1307741567180.600587620621-0.1385200169610.85574983090942.9044363691-49.767970283-56.2150476384
185.278020696481.41586122878-0.9799784440263.54407495461-0.1317014652976.179283713510.00355466507292-0.0600202820106-0.3406450651380.251617919435-0.1660103364950.4980083568560.22767263068-0.561334606993-0.0195741941280.5130030563690.00425059666-0.0171917734420.690693147220.02469183223610.88368337966621.5270101036-26.4572094105-41.4379949214
190.8423726053191.05175483594-0.2714633369694.249659711440.8047707657032.52158877298-0.155978303489-0.3924131330050.00216544521303-0.3779572231110.08285814155950.4281645591930.0526083827063-0.2581269290750.04319343192120.4652471984410.0170384926983-0.04221723547790.616635919612-0.005020768108280.8772866315640.1886147437-58.768037642-64.711380523
202.567276318231.73949818504-0.6392183182493.925892899880.9912020402983.95869171566-0.0260457098776-0.2436607379650.347544890670.642179007142-0.340167769495-0.342511959002-0.0382577885958-0.09294352243960.3957833649690.4999548689780.0250753331597-0.1424458646840.4702144778430.009033026370750.91623485684955.3562364277-51.7588854269-54.5264841412
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 105 )AA2 - 1051 - 104
22chain 'A' and (resid 106 through 127 )AA106 - 127105 - 126
33chain 'A' and (resid 128 through 202 )AA128 - 202127 - 198
44chain 'A' and (resid 203 through 266 )AA203 - 266199 - 262
55chain 'A' and (resid 267 through 342 )AA267 - 342263 - 338
66chain 'A' and (resid 343 through 463 )AA343 - 463339 - 425
77chain 'B' and (resid -1 through 97 )BB-1 - 971 - 99
88chain 'B' and (resid 98 through 127 )BB98 - 127100 - 129
99chain 'B' and (resid 128 through 166 )BB128 - 166130 - 168
1010chain 'B' and (resid 167 through 211 )BB167 - 211169 - 213
1111chain 'B' and (resid 212 through 464 )BB212 - 464214 - 428
1212chain 'C' and (resid 1 through 115 )CC1 - 1151 - 101
1313chain 'C' and (resid 116 through 217 )CC116 - 217102 - 137
1414chain 'C' and (resid 218 through 266 )CC218 - 266138 - 186
1515chain 'C' and (resid 267 through 326 )CC267 - 326187 - 243
1616chain 'C' and (resid 327 through 464 )CC327 - 464244 - 344
1717chain 'D' and (resid 1 through 105 )DD1 - 1051 - 105
1818chain 'D' and (resid 106 through 202 )DD106 - 202106 - 202
1919chain 'D' and (resid 203 through 342 )DD203 - 342203 - 339
2020chain 'D' and (resid 343 through 464 )DD343 - 464340 - 426

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