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

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Basic information

Entry
Database: PDB / ID: 4zqr
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMPDH / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / cytoplasm
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
: / S-1,2-PROPANEDIOL / PHOSPHATE ION / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.692 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 11, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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_label_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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


Theoretical massNumber of molelcules
Total (without water)169,26138
Polymers166,5704
Non-polymers2,69134
Water14,286793
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30330 Å2
ΔGint-103 kcal/mol
Surface area43030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.217, 75.233, 75.291
Angle α, β, γ (deg.)108.30, 108.25, 111.88
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 41642.621 Da / Num. of mol.: 4
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 , 5 types, 827 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / 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: 37.46 %
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-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.692→35.726 Å / Num. obs: 129346 / % possible obs: 91.4 % / Redundancy: 2.2 % / Biso Wilson estimate: 21.38 Å2 / Rsym value: 0.056 / Net I/σ(I): 17.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.6 / % possible all: 51.5

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
SBC-Collectdev_1839data collection
HKL-3000data reduction
HKL-3000phasing
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.692→35.726 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 6432 4.97 %random
Rwork0.1512 ---
obs0.1528 129299 91.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.692→35.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10171 0 165 793 11129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111187
X-RAY DIFFRACTIONf_angle_d1.28215253
X-RAY DIFFRACTIONf_dihedral_angle_d13.4774103
X-RAY DIFFRACTIONf_chiral_restr0.0841812
X-RAY DIFFRACTIONf_plane_restr0.0062008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6916-1.71080.26641070.23812097X-RAY DIFFRACTION46
1.7108-1.7310.24851350.21482559X-RAY DIFFRACTION57
1.731-1.75210.26781610.20912811X-RAY DIFFRACTION63
1.7521-1.77420.23271670.18613198X-RAY DIFFRACTION72
1.7742-1.79760.21512060.18953755X-RAY DIFFRACTION84
1.7976-1.82220.20982080.18124115X-RAY DIFFRACTION92
1.8222-1.84820.24612110.18814264X-RAY DIFFRACTION94
1.8482-1.87580.22412340.17594270X-RAY DIFFRACTION95
1.8758-1.90510.21991910.17494229X-RAY DIFFRACTION95
1.9051-1.93640.19262170.16764375X-RAY DIFFRACTION96
1.9364-1.96980.21882480.16324290X-RAY DIFFRACTION96
1.9698-2.00560.20262350.1674259X-RAY DIFFRACTION96
2.0056-2.04410.20852540.14714397X-RAY DIFFRACTION97
2.0441-2.08590.19722450.1454278X-RAY DIFFRACTION97
2.0859-2.13120.17572060.14584309X-RAY DIFFRACTION97
2.1312-2.18080.18532380.14684450X-RAY DIFFRACTION97
2.1808-2.23530.19072380.14414382X-RAY DIFFRACTION97
2.2353-2.29570.16922040.14074356X-RAY DIFFRACTION97
2.2957-2.36330.20062180.14044399X-RAY DIFFRACTION98
2.3633-2.43950.17482240.14644418X-RAY DIFFRACTION97
2.4395-2.52670.21552330.14754377X-RAY DIFFRACTION98
2.5267-2.62780.17872310.14074392X-RAY DIFFRACTION98
2.6278-2.74740.17452540.14674406X-RAY DIFFRACTION98
2.7474-2.89220.19032270.15154444X-RAY DIFFRACTION98
2.8922-3.07330.19142110.15244345X-RAY DIFFRACTION98
3.0733-3.31040.1652330.14144453X-RAY DIFFRACTION98
3.3104-3.64330.16852230.14574344X-RAY DIFFRACTION97
3.6433-4.16980.15952210.13294387X-RAY DIFFRACTION96
4.1698-5.25080.16432390.14144265X-RAY DIFFRACTION96
5.2508-35.7340.16752130.17184243X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.734-0.3128-0.22750.2527-0.01480.738-0.0549-0.07940.0020.02750.0309-0.00750.0172-0.05490.04820.16730.00720.00840.16210.01950.175917.248333.124556.2392
22.38180.24860.71911.80190.54911.5498-0.0055-0.3566-0.16510.30220.0702-0.11240.0570.0694-0.07810.21050.041-0.02270.24430.04880.15730.676327.417670.5825
31.6957-0.4887-0.28430.50830.35550.59250.01050.0279-0.00590.0198-0.0268-0.03640.0032-0.01140.01850.17990.021-0.01390.16790.01240.167520.712530.480655.3315
43.2481-1.4411-1.93895.02893.27594.78040.0369-0.07540.3475-0.07210.1179-0.5016-0.17530.4906-0.11260.2565-0.0227-0.01050.246-0.00040.261635.411645.806156.3605
51.4306-0.09230.41071.08220.06532.4666-0.0286-0.05720.05840.00840.04210.0414-0.0933-0.1247-0.03150.1360.03360.00140.14970.00390.16119.225840.40254.5874
60.52780.2713-0.88831.7428-0.23123.5265-0.12990.01220.230.0819-0.0889-0.2176-0.53110.5990.1290.3243-0.0347-0.03290.32990.03370.306516.17854.970146.6686
75.3444-2.383-3.2531.28381.60852.3703-0.2147-0.0024-0.20870.11640.02270.13590.3084-0.04740.28940.2206-0.0067-0.01870.18650.01210.18459.666128.127424.6277
82.2338-1.36180.342.629-0.39351.24150.12180.32730.1674-0.3272-0.1251-0.0342-0.10040.01250.00740.23450.02660.01550.25490.03460.148914.617845.6068-5.3067
91.026-0.3385-0.16591.41630.0130.74610.00130.1435-0.0318-0.11610.00150.1392-0.029-0.03960.00710.15390.015-0.01570.18090.01540.16136.812837.90526.2626
104.6199-0.4349-3.41213.27460.17934.70540.1566-0.03690.57620.0120.0225-0.1774-0.57370.0386-0.13130.2883-0.0289-0.00240.24180.00760.253920.064955.923610.2582
111.3077-0.21610.04963.5772-1.26062.82660.06740.19140.142-0.406-0.1085-0.27750.03390.23130.04390.16360.03310.02980.25180.01730.195529.931133.75065.4472
121.7210.17510.70191.03410.14433.3475-0.0193-0.01210.13620.0476-0.0132-0.1047-0.23960.15660.00290.17150.0493-0.00790.14770.01510.184127.872132.450817.9689
136.88932.24745.13141.20181.9273.9250.3188-0.5249-0.64750.1655-0.09250.00040.3359-0.3485-0.31330.2156-0.023-0.00850.21080.03750.22712.54512222.8952
141.0296-0.0462-0.62430.4906-0.09431.8269-0.04710.0482-0.0493-0.0712-0.0247-0.14990.18920.29920.07580.20170.0450.01440.22910.00280.222548.713117.937524.9271
150.62410.16770.12440.807-0.33041.9758-0.01010.0076-0.036-0.04690.0251-0.09560.07510.0427-0.02340.14410.01740.00850.1666-0.00610.154535.826318.200326.0477
165.107-0.72673.29921.8399-1.03954.5669-0.03830.31250.3997-0.1425-0.0723-0.1891-0.33850.32780.02360.2292-0.01920.01170.24510.03170.282546.980937.701824.2138
173.50950.5234-1.43642.007-0.54732.2341-0.1088-0.3046-0.140.0734-0.0581-0.29010.03340.3937-0.00370.17110.0263-0.03870.24740.00590.171543.685824.433144.4744
182.1681-0.944-0.13882.53440.80071.64850.05570.01370.2397-0.0639-0.0563-0.0764-0.21030.0476-0.01780.18430.00660.02580.20520.03110.138131.963829.798543.3129
190.6566-0.40150.37850.1769-0.28091.16180.05250.0229-0.0947-0.0406-0.01660.08020.0549-0.0847-0.06890.1373-0.0139-0.00850.1388-0.00230.1533-2.143740.384233.0228
202.3766-0.29670.35262.04390.09545.266-0.01340.01050.3752-0.0141-0.04690.0877-0.6758-0.22590.06630.25980.0587-0.00440.15090.00070.2498-7.555966.762642.1807
212.5883-0.937-0.08414.57060.5351.51270.0041-0.11480.19130.3787-0.08150.2755-0.0412-0.37460.03610.1960.03730.04480.2595-0.03450.1675-13.966256.008151.4978
221.0753-0.36950.24231.03-0.21741.76130.0109-0.00030.19380.0243-0.0432-0.0288-0.16710.02520.00670.14110.02080.01010.13470.00380.1321-1.49351.148139.8278
231.53340.19121.6382.1535-0.01652.5059-0.1712-0.20540.18280.1464-0.0001-0.091-0.5035-0.19520.13020.14220.06460.03970.2270.01170.20233.70457.99237.0852
242.8474-0.5492-0.65221.0636-0.01011.24360.0051-0.06570.2361-0.04750.0217-0.1265-0.06840.1328-0.03640.20230.012-0.00960.1856-0.01480.16116.795146.260723.2744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 326 )
3X-RAY DIFFRACTION3chain 'A' and (resid 327 through 396 )
4X-RAY DIFFRACTION4chain 'A' and (resid 397 through 469 )
5X-RAY DIFFRACTION5chain 'A' and (resid 470 through 512 )
6X-RAY DIFFRACTION6chain 'A' and (resid 513 through 528 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 60 )
8X-RAY DIFFRACTION8chain 'B' and (resid 61 through 275 )
9X-RAY DIFFRACTION9chain 'B' and (resid 276 through 396 )
10X-RAY DIFFRACTION10chain 'B' and (resid 397 through 469 )
11X-RAY DIFFRACTION11chain 'B' and (resid 470 through 488 )
12X-RAY DIFFRACTION12chain 'B' and (resid 489 through 528 )
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 46 )
14X-RAY DIFFRACTION14chain 'C' and (resid 47 through 303 )
15X-RAY DIFFRACTION15chain 'C' and (resid 304 through 396 )
16X-RAY DIFFRACTION16chain 'C' and (resid 397 through 469 )
17X-RAY DIFFRACTION17chain 'C' and (resid 470 through 488 )
18X-RAY DIFFRACTION18chain 'C' and (resid 489 through 528 )
19X-RAY DIFFRACTION19chain 'D' and (resid 27 through 82 )
20X-RAY DIFFRACTION20chain 'D' and (resid 83 through 125 )
21X-RAY DIFFRACTION21chain 'D' and (resid 126 through 303 )
22X-RAY DIFFRACTION22chain 'D' and (resid 304 through 422 )
23X-RAY DIFFRACTION23chain 'D' and (resid 423 through 488 )
24X-RAY DIFFRACTION24chain 'D' and (resid 489 through 528 )

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