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- PDB-5mcp: Structure of IMP dehydrogenase from Ashbya gossypii bound to ATP -

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Basic information

Entry
Database: PDB / ID: 5mcp
TitleStructure of IMP dehydrogenase from Ashbya gossypii bound to ATP
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMP dehydrogenase / Ashbya gossypii / allosteric modulator / purine nucleotides
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS 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 / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / 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
ADENOSINE-5'-TRIPHOSPHATE / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesAshbya gossypii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWinter, G. / Fernandez-Justel, D. / de Pereda, J.M. / Revuelta, J.L. / Buey, R.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-79237-P Spain
CitationJournal: Sci Rep / Year: 2017
Title: A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases.
Authors: Buey, R.M. / Fernandez-Justel, D. / Marcos-Alcalde, I. / Winter, G. / Gomez-Puertas, P. / de Pereda, J.M. / Luis Revuelta, J.
History
DepositionNov 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conf
Item: _pdbx_audit_support.funding_organization / _struct_conf.beg_auth_comp_id ..._pdbx_audit_support.funding_organization / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

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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
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,68340
Polymers453,3178
Non-polymers12,36732
Water22,9871276
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44050 Å2
ΔGint-296 kcal/mol
Surface area136930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.891, 152.090, 152.255
Angle α, β, γ (deg.)90.00, 93.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 56664.574 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus)
Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: AGOS_AER117W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q756Z6, IMP dehydrogenase
#2: Chemical...
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1276 / 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: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Imidazole + 0.05 M Mes; pH 6.5 20 % Glycerol 20 % PEG-4000 0.02 M D-glucose 0.02 M D-Mannose 0.02 M D_Galactose 0.02 M L-Fucose 0.02 M C-Xylose 0.02 M N-Acetyl-D-Glucosamine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.4→152.042 Å / Num. obs: 226714 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.206 / Net I/σ(I): 5.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.487 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.686 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z0G

4z0g


Resolution: 2.4→152.042 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 11355 5.02 %
Rwork0.2494 --
obs0.2505 226233 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→152.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22478 0 752 1276 24506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323593
X-RAY DIFFRACTIONf_angle_d0.58832138
X-RAY DIFFRACTIONf_dihedral_angle_d12.73913743
X-RAY DIFFRACTIONf_chiral_restr0.0433799
X-RAY DIFFRACTIONf_plane_restr0.0044078
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)
11.24880.7623-0.54970.961-0.88681.13210.07760.0688-0.07220.11390.12640.1183-0.0241-0.33840.02990.236-0.0162-0.01390.25380.05950.1723-6.1652-36.309-22.8315
21.48290.5691-0.75981.8592-0.14620.3142-0.19080.1717-0.2789-0.25260.12180.16350.0349-0.2662-0.00750.5713-0.0922-0.02410.38740.08140.3354-11.1208-49.9645-17.1644
31.0760.6758-0.33911.5378-0.00991.81810.06720.0280.01650.06030.05070.04640.0167-0.1114-0.0010.40140.0264-0.01110.20140.04570.16776.5886-24.5058-21.0567
41.2257-0.7830.61913.1021-0.55891.44890.06130.1279-0.0731-0.0203-0.1276-0.5642-0.05810.21870.08660.35950.02620.04290.24980.01020.227721.5731-11.4018-20.5173
51.269-0.6017-0.61490.66740.74270.95780.0732-0.0329-0.0606-0.0777-0.26220.368-0.0005-0.2782-0.00750.4267-0.01830.0070.3152-0.11370.3519-14.148819.86940.1078
61.0659-0.6616-0.69020.55650.48791.2487-0.0369-0.1905-0.07510.1123-0.00310.32410.1319-0.16150.03660.5753-0.05950.07230.3954-0.05390.324-12.526120.20289.2904
70.9687-0.3345-0.67622.2328-0.11181.41420.0563-0.0204-0.05020.0319-0.09630.1625-0.0571-0.053-0.00950.4239-0.0021-0.03270.2217-0.04280.16726.166115.0518-14.8665
81.3230.48210.55311.2610.52043.21010.031-0.0129-0.0498-0.02570.153-0.23940.37290.6859-0.10350.4050.0465-0.01440.243-0.02890.191121.923414.8037-27.3715
91.4292-0.91880.42731.0903-1.48390.73940.0467-0.01250.08750.12630.23420.29730.1037-0.515-0.00640.44780.04470.03260.43280.10370.3089-11.639437.4109-60.4723
101.1437-0.4350.92111.0772-0.49310.7136-0.2139-0.1840.25850.37650.12250.1449-0.1435-0.3478-0.01910.63370.06510.04140.42230.04480.3661-8.99646.4205-60.3576
111.2022-0.74860.17931.57540.13952.29670.0413-0.0380.0127-0.04760.05560.03580.0277-0.10550.01080.4026-0.03430.00790.17450.05640.15568.202521.2731-54.3424
120.960.72830.68561.88091.05450.8472-0.01550.00680.0303-0.2098-0.11010.17330.0163-0.0324-0.01630.40460.0076-0.00380.22-0.0010.18635.6171-12.4897-66.2322
131.47760.51250.83441.54580.30731.2903-0.05380.12840.1651-0.0642-0.0950.7727-0.1216-0.3628-0.01550.47060.0723-0.09510.4274-0.12120.575-16.9307-26.1436-87.9998
140.93540.41710.66321.79340.24721.56040.05460.04330.0607-0.0001-0.11080.1228-0.0047-0.0363-0.00770.38220.00680.03120.2078-0.04580.17028.5814-18.2379-60.5974
150.9756-0.3075-0.56420.61910.20370.38070.1173-0.0753-0.27460.3323-0.68240.15990.2037-0.6941-0.06070.8222-0.1113-0.00620.9878-0.12861.083-89.278-14.9284-24.0037
160.4102-0.81560.68622.3429-0.41252.2082-0.1092-0.46540.63530.79670.44110.0920.0879-0.2653-0.06980.44780.0384-0.14770.81460.12991.2421-76.2065-19.0223-34.4269
170.2215-0.08180.43180.58820.00610.94920.484-0.32970.06140.21220.0658-0.09310.56770.2558-0.00780.83280.1595-0.22650.9399-0.03521.261-64.9286-38.8929-41.1152
180.99740.6101-0.62581.2719-0.74232.101-0.14150.4111-0.2977-0.12090.2414-0.65580.1692-0.1021-0.06660.51510.2434-0.16941.019-0.03761.4317-56.9711-43.6527-53.1675
190.268-0.17190.1540.14580.13030.60180.54040.1775-0.8704-0.4695-0.34310.4563-0.6660.19020.00480.863-0.0255-0.32231.2643-0.03760.9812-41.122-59.3999-35.7835
201.2665-0.13520.18731.0684-0.21360.62090.1450.13240.27640.2953-0.1355-0.76420.27620.3755-0.04790.82380.0856-0.17851.03360.021.2423-72.6073-36.4534-54.1227
211.424-0.4112-0.65490.12510.11540.35960.05110.013-0.04330.30990.13970.1116-0.1241-0.1226-0.05040.75370.1488-0.16710.99140.10260.9727-62.6838-30.0229-40.2074
220.749-0.71660.04870.6759-0.04730.52440.2897-0.315-0.44410.8488-0.15120.30220.4953-0.4357-0.01010.84920.113-0.23250.75380.0131.23-73.8631-28.7039-30.9804
230.00370.08160.07850.9510.70130.93380.4287-0.38990.336-0.1601-0.150.6705-0.836-0.6983-0.09330.67970.16940.26240.82970.3491.4224-89.123215.9955-32.7
240.10150.38850.13371.02130.17270.62250.6238-0.4590.09580.06680.5771-0.9405-0.15360.57120.04630.8559-0.11680.17941.0991-0.01861.3323-76.98124.1967-20.1231
250.5594-0.2346-0.39940.07930.16290.31360.40460.5988-0.07440.0102-0.09180.26960.2446-0.66130.22570.6569-0.4021-0.30780.87240.13421.6536-52.6282-6.25972.6979
260.5710.9866-0.05031.7199-0.44662.3654-0.2942-0.74450.20750.39930.17810.39830.40760.38650.01291.0784-0.11720.03310.84380.15561.2891-33.50732.921520.3797
270.26520.13370.06220.0880.04370.11420.0633-0.23640.2715-0.12650.0414-0.0418-0.1404-0.01880.20080.7527-0.70740.66991.1384-0.12462.0222-55.7312.077812.3308
280.4368-0.0451-0.11210.1651-0.19940.33070.0695-0.22730.08270.16540.26060.1209-0.2510.5664-0.0670.5696-0.0488-0.23061.061-0.04661.1629-73.8484-17.5901-6.5517
291.5212-0.15070.85311.4907-0.20741.69360.048-0.17650.40240.37310.1061-0.3651-0.4630.2740.0220.8531-0.085-0.09150.8309-0.09981.4654-78.8794-9.7268-19.6901
300.6390.7648-0.26261.11720.09770.93180.63910.31880.70750.2332-0.32990.5872-0.94810.1010.08020.7207-0.3340.1871.0091-0.05371.5083-74.31494.9277-18.2223
310.97750.0175-0.04220.7184-0.00850.6618-0.01410.27680.091-0.4828-0.0816-0.17870.29390.3275-0.04050.69230.13580.13061.05440.22731.1499-72.2321-10.6943-67.8443
320.9225-0.0556-0.22960.15830.21730.26250.65370.45340.30150.2001-0.1372-0.4865-0.1421-0.7124-0.0390.98620.1947-0.08230.99120.18771.7608-37.8876-3.9335-97.0247
331.0607-1.1079-0.47611.09580.54650.16330.07220.03580.26271.00150.03420.0612-0.0448-0.1395-0.08280.85760.16730.25231.01440.21881.528-65.15956.6798-84.9764
340.66490.2514-0.34020.9482-0.11620.83690.50540.08320.2201-0.361-0.2458-0.1123-0.59060.0686-0.03950.98220.04320.09161.03560.07441.167-71.4431-5.2811-69.0156
350.6123-0.3659-0.01780.58270.12560.3276-0.19060.28780.2773-0.2124-0.4397-0.2045-0.3484-0.19790.09940.47290.09640.2231.15650.18481.5011-84.38588.6177-60.6875
360.5191-0.01570.20140.5172-0.21730.232-0.17240.30940.8184-0.15370.1036-0.3425-0.3909-0.7769-0.03681.0352-0.0790.41910.98080.00831.5033-69.452328.4925-47.7212
370.0277-0.1675-0.02371.03560.1130.0436-0.104-0.3921-0.29530.0506-0.44351.10520.05160.0886-0.27030.8285-0.19340.45471.1044-0.00421.217-51.035643.3436-37.6332
380.66-0.4249-0.85271.76110.33731.25690.3473-0.36370.74590.35710.06310.28410.1167-0.2318-0.04981.09220.02720.19621.5698-0.13560.8123-31.207556.2501-43.1162
391.0538-0.08172.0260.3364-0.04943.9421-0.54690.08810.72420.066-0.4249-0.033-0.1889-0.151-0.41980.66610.39940.42541.34590.12551.4438-44.426857.4543-52.8747
401.14990.2778-0.1860.1492-0.6854.62840.3265-0.41751.16840.0011-0.0214-0.1906-0.3658-0.291-0.11190.8241-0.05030.39510.5488-0.09191.8997-66.06743.1278-38.0759
410.7052-0.25520.25390.8139-0.03660.71920.6920.03260.2116-0.2302-0.2085-0.2023-0.2482-0.0435-0.06111.0595-0.09570.39820.7509-0.00471.4798-75.058825.5631-38.8732
421.2009-1.11560.49521.26330.15721.7568-0.02940.5798-0.23790.1855-0.02160.65860.68670.55970.18720.62470.21140.41620.8260.07141.7419-80.82219.8826-54.9608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 195 )
2X-RAY DIFFRACTION2chain 'A' and (resid 196 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 507 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 37 )
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 195 )
6X-RAY DIFFRACTION6chain 'B' and (resid 196 through 256 )
7X-RAY DIFFRACTION7chain 'B' and (resid 257 through 507 )
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 37 )
9X-RAY DIFFRACTION9chain 'C' and (resid 38 through 195 )
10X-RAY DIFFRACTION10chain 'C' and (resid 196 through 256 )
11X-RAY DIFFRACTION11chain 'C' and (resid 257 through 507 )
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 132 )
13X-RAY DIFFRACTION13chain 'D' and (resid 133 through 256 )
14X-RAY DIFFRACTION14chain 'D' and (resid 257 through 507 )
15X-RAY DIFFRACTION15chain 'E' and (resid 4 through 27 )
16X-RAY DIFFRACTION16chain 'E' and (resid 28 through 51 )
17X-RAY DIFFRACTION17chain 'E' and (resid 52 through 90 )
18X-RAY DIFFRACTION18chain 'E' and (resid 91 through 113 )
19X-RAY DIFFRACTION19chain 'E' and (resid 114 through 238 )
20X-RAY DIFFRACTION20chain 'E' and (resid 239 through 372 )
21X-RAY DIFFRACTION21chain 'E' and (resid 373 through 459 )
22X-RAY DIFFRACTION22chain 'E' and (resid 460 through 499 )
23X-RAY DIFFRACTION23chain 'F' and (resid 4 through 27 )
24X-RAY DIFFRACTION24chain 'F' and (resid 28 through 67 )
25X-RAY DIFFRACTION25chain 'F' and (resid 69 through 165 )
26X-RAY DIFFRACTION26chain 'F' and (resid 166 through 196 )
27X-RAY DIFFRACTION27chain 'F' and (resid 197 through 238 )
28X-RAY DIFFRACTION28chain 'F' and (resid 239 through 319 )
29X-RAY DIFFRACTION29chain 'F' and (resid 320 through 360 )
30X-RAY DIFFRACTION30chain 'F' and (resid 361 through 499 )
31X-RAY DIFFRACTION31chain 'G' and (resid 3 through 102 )
32X-RAY DIFFRACTION32chain 'G' and (resid 103 through 206 )
33X-RAY DIFFRACTION33chain 'G' and (resid 207 through 309 )
34X-RAY DIFFRACTION34chain 'G' and (resid 310 through 501 )
35X-RAY DIFFRACTION35chain 'H' and (resid 3 through 40 )
36X-RAY DIFFRACTION36chain 'H' and (resid 41 through 81 )
37X-RAY DIFFRACTION37chain 'H' and (resid 82 through 142 )
38X-RAY DIFFRACTION38chain 'H' and (resid 143 through 184 )
39X-RAY DIFFRACTION39chain 'H' and (resid 185 through 228 )
40X-RAY DIFFRACTION40chain 'H' and (resid 234 through 268 )
41X-RAY DIFFRACTION41chain 'H' and (resid 269 through 478 )
42X-RAY DIFFRACTION42chain 'H' and (resid 479 through 499 )

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