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- PDB-7qbj: bacterial IMPDH chimera -

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Basic information

Entry
Database: PDB / ID: 7qbj
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
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: 2.27 Å
AuthorsLabesse, G. / Gelin, M. / Munier-Lehmann, H. / Gedeon, A. / Haouz, A.
Funding support France, 4items
OrganizationGrant numberCountry
Pasteur Institute France
Centre National de la Recherche Scientifique (CNRS) France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-0005 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 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_audit_support / struct_keywords
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
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


Theoretical massNumber of molelcules
Total (without water)216,1224
Polymers216,1224
Non-polymers00
Water10,629590
1
A: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase

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

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

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


Theoretical massNumber of molelcules
Total (without water)432,2458
Polymers432,2458
Non-polymers00
Water1448
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 area33550 Å2
ΔGint-143 kcal/mol
Surface area137200 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase

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

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

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


Theoretical massNumber of molelcules
Total (without water)432,2458
Polymers432,2458
Non-polymers00
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 area31360 Å2
ΔGint-188 kcal/mol
Surface area125440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.041, 145.041, 120.099
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
Components on special symmetry positions
IDModelComponents
11C-621-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M TRIS 8.5 pH, 8 %w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.27→48.32 Å / Num. obs: 117473 / % possible obs: 99.7 % / Redundancy: 14 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1671 / Rrim(I) all: 0.173 / Net I/av σ(I): 10.07 / Net I/σ(I): 10.07
Reflection shellResolution: 2.27→2.4 Å / Num. unique obs: 18121 / CC1/2: 0.794 / Rrim(I) all: 0.891 / Rsym value: 0.859

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Processing

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

4dqw


Resolution: 2.27→48.32 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.1087
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2264 11565 5.05 %
Rwork0.193 217541 -
obs0.197 116298 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.03 Å2
Refinement stepCycle: LAST / Resolution: 2.27→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12085 0 0 590 12675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009112256
X-RAY DIFFRACTIONf_angle_d1.041516520
X-RAY DIFFRACTIONf_chiral_restr0.05881962
X-RAY DIFFRACTIONf_plane_restr0.01062149
X-RAY DIFFRACTIONf_dihedral_angle_d5.90731765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.30.33475110.37419960X-RAY DIFFRACTION86.35
2.3-2.340.37645950.372710876X-RAY DIFFRACTION94.71
2.34-2.380.41165040.355711087X-RAY DIFFRACTION95.59
2.38-2.430.36126480.330410812X-RAY DIFFRACTION94.26
2.43-2.480.31316580.32410824X-RAY DIFFRACTION94.24
2.48-2.540.32344930.316710989X-RAY DIFFRACTION95.64
2.54-2.610.27814860.287811022X-RAY DIFFRACTION95.75
2.61-2.680.30755380.268710963X-RAY DIFFRACTION95.3
2.68-2.750.29355500.255410953X-RAY DIFFRACTION95.22
2.75-2.840.27445840.248610912X-RAY DIFFRACTION94.92
2.84-2.950.24326160.228810940X-RAY DIFFRACTION94.67
2.95-3.060.25375940.217610893X-RAY DIFFRACTION94.81
3.06-3.20.22055800.211310939X-RAY DIFFRACTION94.96
3.2-3.370.22046400.195110872X-RAY DIFFRACTION94.44
3.37-3.580.2314860.182410963X-RAY DIFFRACTION95.76
3.58-3.860.19346170.16710922X-RAY DIFFRACTION94.65
3.86-4.250.18616360.146310914X-RAY DIFFRACTION94.49
4.25-4.860.17455410.130810933X-RAY DIFFRACTION95.28
4.86-6.120.21476580.152210857X-RAY DIFFRACTION94.29
6.12-48.320.20186190.169910921X-RAY DIFFRACTION94.63
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)
10.4490749983380.2482081682710.2496653257511.176554851010.3452037742870.620931336743-0.0345763473648-0.106412978470.06735450635230.0889062788253-0.04236616434770.05131478203610.00519453879583-0.04586632814210.07784947694070.265429564189-0.03090434565650.001986643438720.3020048036460.001568946840250.3756667174516.476573536432.582011565818.9521267555
21.40404718593-0.3020766401820.5042461791762.130654688730.9663409634396.7967019546-0.1284954427030.1350333255190.254845222496-0.112229590181-0.02020374330730.0967164264072-0.545156207577-0.1621264375490.1527782138860.321670483138-0.0619819723569-0.03016183452260.3189901823850.0287777748360.36195064267534.131554209157.97847581735.0764592842
33.229135711951.800532542261.733604723761.883005183071.326159432371.852936787450.0500853309399-0.005711099068190.2495779252160.0253800108542-0.05626852002860.131798548408-0.0252644819811-0.07643131338450.04841495776940.2560806479240.004022815986740.02261814041670.2320403143570.03295841743360.3415470977177.1651785804733.8182786569.66160450966
41.62996126702-0.765420506881-0.05663662178121.45579199651.370493874063.44743097782-0.0460605574867-0.28714923279-0.194104835850.189504751837-0.005525446998730.008829874875410.149228091693-0.0833654976620.03678503412340.312931012548-0.0320837040356-0.003689680299370.3091833305660.06848871103660.37682894085216.362333767519.566294020220.6957400756
51.26591304104-0.184213981325-0.07228099152991.078586006450.1296200206820.8030783631560.04773665818530.172718612378-0.107080512391-0.105393970791-0.0429999519166-0.04176006920790.0458277767407-0.07770047550920.0230944172310.276976251049-0.002586405075220.01074997374750.2972576709920.00833173033240.25598432656857.71184640949.42669896652.51192596059
60.2937312669721.331875280021.710231910126.085558231147.134890204668.13366431740.364194427292-0.0659756158360.00775061230301-0.218994726349-0.4957757064470.1567862058680.154096741729-0.6075355019770.2261568740470.526699106697-0.0939889083676-0.1183017719330.578687195991-0.07241646128960.47965125852938.330051356826.0796928262-20.3897310557
75.24395865154-0.407048741687-0.116121238484.339328305621.656519087024.209737393910.073199261219-0.445506527343-0.3304645861880.933449566254-0.499086179390.002630051988791.21192950311-0.8880706399690.08594155295441.02494697179-0.208306019631-0.2506322979560.789476532466-0.2055720638420.74636498645639.175455951912.4626897803-16.7184629442
81.1147365474-0.150608534012-0.129060391636.553013558813.206829890683.573773676650.03635949937530.345076072847-0.215756283708-0.260774122532-0.0941062625730.3098145553980.197026492286-0.2399450529350.09102208238490.291503027263-0.0506442560395-0.02871516235660.336441262071-0.02542480292540.26807704688443.309845119942.25271223581.47551923735
94.16461396569-0.5406103183161.443895804795.839940663421.646553964711.06950298235-0.08074424957530.3175177925020.295861273034-0.6634953424420.00952914197659-0.770689170911-0.1723624066650.134053798147-0.06172623449030.295416626238-0.02245068450560.03803563308280.303102152079-0.04657369524070.27863115635554.521875586660.45702567795.65618218202
101.91196229596-0.790962196313-0.6876996205731.45779385270.8093644777763.240692305840.07236140707350.3762875705650.0539855254107-0.264684994281-0.135020700855-0.116069910898-0.0460594069663-0.1274208257110.08283026821430.241855135481-0.007491332897090.03070362759320.2847649750360.002842035392110.25576686341862.340216875548.5768903451-3.81634414243
111.3868374243-0.431303060938-0.2174253990380.7405072174080.04996782503850.842147852915-0.0765470606528-0.190404951832-0.1403445445560.06797309539140.01850268724650.05246340729620.07556188433010.04747104022020.06052722017810.331625104162-0.02152492284190.01307707319180.326226716575-0.01656014801230.2683922712667.437898955844.5088789786-48.2213135748
121.84280665192.75004728073-2.34411405674.01976909069-3.479513985612.936390588420.454750672449-0.72620899976-0.01484818612230.43224947662-0.368534461995-0.1340402762660.1953108313340.3923453093960.4225411326610.644018548335-0.003410021042010.0500303759170.5094640199690.1829741246630.50941046066670.341153554920.6787000421-31.1160574417
132.634899452113.06675173808-2.535302670213.77250760736-2.831050283452.39442326952-0.2508554061510.1989953106150.0343226323163-0.3531453160860.1478973424870.1766625994040.128047362858-0.116177668316-0.006271826855630.501188867197-0.04671504730070.01672841033890.460595430984-0.005716024800590.53864412270254.532630468816.909932706-39.1463059442
142.984921501410.874093410886-0.6348262307244.37088480596-1.310596722162.31315858706-0.0468539771539-0.0716651141414-0.2006130442050.03982362833930.00510557714642-0.04561560690540.2365779259540.1519996245740.07081324105410.2903561798760.01456738882090.04446146403610.291661067056-0.005033821966920.23242949888780.272438159139.5839598738-53.5326848306
153.20153420264-0.316308367186-0.1172725240011.38781702674-0.7815080468393.9028101187-0.086498753566-0.5296609970940.07704658362170.232475297388-0.002427558202280.1121898460120.02824630477240.1647217367240.1134294328890.3116919005710.001114367676090.02457635461770.325776167828-0.05258455690490.26237060331263.708898090448.4271969992-40.7925569729
162.13604598011-0.576937095467-0.373835608011.56653888517-0.04084328497711.39260616261-0.06564457452-0.0479303265661-0.132069312023-0.2735375411990.1379441919820.004198747819610.16441505628-0.04217241101760.005128931552240.366537311491-0.03567406806760.01401131485480.355260297393-0.06549627517690.3369005034668.947441845459.9262730708472.5605397058
171.2444991431.21121906913-1.017161976581.01421168013-0.961891881511.28800188105-0.0220622690084-0.105385333751-0.149170122786-0.164729605331-0.0951971013604-0.1105644633340.01383035507110.1963433962920.1791157062940.407648134138-0.00153785258059-0.007953176163070.399308848470.01105221392970.48089366159335.107260226725.37021764354.0293658569
185.120410304710.0714465199701-2.648731328732.129923562640.8942390157282.185696123150.04034029515410.1708811623350.216514329324-0.2333442809990.0464232727133-0.370065567247-0.06299124975020.797999648813-0.07896391619910.414114795242-0.006693074926910.01137023662040.545877187214-0.05533163039010.4478642769356.794502483846.606549246135.0941547328
194.33735459405-0.409492099158-3.168284737933.155092107090.6005084352629.28532241155-0.150525583821-0.207676923097-0.1112213184950.09898632012890.0840037175775-0.1095372648740.6962401770320.337668978310.08122044790330.3697528742450.00582276681897-0.05488918421040.286747548345-0.0439217901480.29906956282745.336507467344.807679289650.7872985094
202.350677983550.603295872826-0.4302226568548.28617751008-1.696389506242.893535293110.02506107117250.003241082163470.17343010047-0.0566360174931-0.191517271724-0.704274726952-0.03592882241360.4210147191450.1986101068290.319272584492-0.03689273023-0.01102667232840.3926642398820.02072203634460.3161858681238.084120668623.14898984659.5602627364
212.086465802441.08039399935-1.537898256825.162893191-1.719416835272.15851211279-0.001047059442610.08993105856040.07000750502560.031725772399-0.0055203514673-0.0260633189210.002670642360310.1463090690640.05812033900060.2951785397670.000781640214522-0.05870611689920.3352741273620.01193619737090.27661256938329.69800653679.0001187492969.7395130601
221.52138639835-0.415974398742-1.123445104821.90097976082-1.271525076763.65547866433-0.05734577979580.1016495065370.00178793962113-0.325013295979-0.05829854949760.1176287950850.1023755021970.02300418656890.108449682830.366544609632-0.0165595541489-0.05274980866560.369147303927-0.01971094977740.3366793174516.416841623119.484489908556.1128411211
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 105 )AA1 - 1051 - 105
22chain 'A' and (resid 106 through 202 )AA106 - 202106 - 199
33chain 'A' and (resid 203 through 337 )AA203 - 337200 - 333
44chain 'A' and (resid 338 through 464 )AA338 - 464334 - 427
55chain 'B' and (resid -3 through 75 )BB-3 - 751 - 79
66chain 'B' and (resid 76 through 115 )BB76 - 11580 - 119
77chain 'B' and (resid 116 through 190 )BB116 - 190120 - 190
88chain 'B' and (resid 191 through 289 )BB191 - 289191 - 289
99chain 'B' and (resid 290 through 326 )BB290 - 326290 - 325
1010chain 'B' and (resid 327 through 464 )BB327 - 464326 - 429
1111chain 'C' and (resid 0 through 75 )CC0 - 751 - 76
1212chain 'C' and (resid 76 through 116 )CC76 - 11677 - 99
1313chain 'C' and (resid 117 through 218 )CC117 - 218100 - 133
1414chain 'C' and (resid 219 through 337 )CC219 - 337134 - 247
1515chain 'C' and (resid 338 through 464 )CC338 - 464248 - 341
1616chain 'D' and (resid 0 through 24 )DD0 - 241 - 25
1717chain 'D' and (resid 25 through 105 )DD25 - 10526 - 106
1818chain 'D' and (resid 106 through 154 )DD106 - 154107 - 155
1919chain 'D' and (resid 155 through 202 )DD155 - 202156 - 203
2020chain 'D' and (resid 203 through 238 )DD203 - 238204 - 239
2121chain 'D' and (resid 239 through 337 )DD239 - 337240 - 338
2222chain 'D' and (resid 338 through 464 )DD338 - 464339 - 432

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