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- PDB-6mgr: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

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Basic information

Entry
Database: PDB / ID: 6mgr
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor Oxanosine monophosphate
ComponentsInosine monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IMPDH / TIM barrel / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / 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
Chem-JQS / : / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKim, Y. / Maltseva, N. / Yu, R. / Hedstrom, L. / 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: To Be Published
Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor Oxanosine Monophosphate
Authors: Kim, Y. / Maltseva, N. / Yu, R. / Hedstrom, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine monophosphate dehydrogenase
B: Inosine monophosphate dehydrogenase
C: Inosine monophosphate dehydrogenase
D: Inosine monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,21543
Polymers164,2134
Non-polymers4,00239
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26240 Å2
ΔGint-425 kcal/mol
Surface area49650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.343, 119.592, 119.307
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Inosine monophosphate dehydrogenase / IMP dehydrogenase


Mass: 41053.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: C9J79_08320 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2R4D3F6, IMP dehydrogenase

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Non-polymers , 6 types, 467 molecules

#2: Chemical
ChemComp-JQS / 5-[(Z)-(aminomethylidene)amino]-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid


Mass: 366.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Lithium Sulfate, 0.1 M MES:NaOH pH 6, 35% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 135052 / % possible obs: 98.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 17
Reflection shellResolution: 1.97→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 1 / Num. unique obs: 5909 / CC1/2: 0.591 / % possible all: 86.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 5URQ
Resolution: 1.97→45.284 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 23.88
RfactorNum. reflection% reflection
Rfree0.2018 6506 4.84 %
Rwork0.1734 --
obs0.1749 134425 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.2 Å2
Refinement stepCycle: LAST / Resolution: 1.97→45.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10843 0 220 428 11491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711300
X-RAY DIFFRACTIONf_angle_d0.9615256
X-RAY DIFFRACTIONf_dihedral_angle_d16.3086828
X-RAY DIFFRACTIONf_chiral_restr0.0531753
X-RAY DIFFRACTIONf_plane_restr0.0041942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9662-1.98860.41661640.35973202X-RAY DIFFRACTION74
1.9886-2.0120.35941900.32113684X-RAY DIFFRACTION86
2.012-2.03650.35141780.3053969X-RAY DIFFRACTION90
2.0365-2.06230.2951910.28334129X-RAY DIFFRACTION94
2.0623-2.08940.27962220.25674197X-RAY DIFFRACTION96
2.0894-2.1180.29861980.24424230X-RAY DIFFRACTION98
2.118-2.14830.24652240.24044314X-RAY DIFFRACTION98
2.1483-2.18040.26372780.22984297X-RAY DIFFRACTION99
2.1804-2.21440.28262190.22114266X-RAY DIFFRACTION99
2.2144-2.25070.23522190.19214355X-RAY DIFFRACTION100
2.2507-2.28960.20231770.18734390X-RAY DIFFRACTION99
2.2896-2.33120.22012210.1984350X-RAY DIFFRACTION100
2.3312-2.3760.25441900.18284415X-RAY DIFFRACTION100
2.376-2.42450.20951980.18854359X-RAY DIFFRACTION100
2.4245-2.47720.21771850.1884413X-RAY DIFFRACTION100
2.4772-2.53490.24232070.18854352X-RAY DIFFRACTION100
2.5349-2.59820.2382150.19544365X-RAY DIFFRACTION100
2.5982-2.66850.25412600.18324289X-RAY DIFFRACTION99
2.6685-2.7470.24882080.19254290X-RAY DIFFRACTION99
2.747-2.83560.25592120.20344376X-RAY DIFFRACTION100
2.8356-2.9370.2131790.20274465X-RAY DIFFRACTION100
2.937-3.05450.2122190.20214363X-RAY DIFFRACTION100
3.0545-3.19350.23362630.19614320X-RAY DIFFRACTION100
3.1935-3.36180.21662640.18564314X-RAY DIFFRACTION99
3.3618-3.57240.21372300.16534348X-RAY DIFFRACTION99
3.5724-3.84810.16762050.15484431X-RAY DIFFRACTION100
3.8481-4.23510.15742170.144380X-RAY DIFFRACTION100
4.2351-4.84730.16612170.13344373X-RAY DIFFRACTION100
4.8473-6.10470.18073210.15714300X-RAY DIFFRACTION99
6.1047-45.29640.18372350.16344383X-RAY DIFFRACTION98
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)
11.5642-0.5684-0.78680.85240.33583.4969-0.0645-0.0634-0.14490.091-0.00520.23130.1641-0.1650.13390.4275-0.0470.03880.41950.01740.447620.44359.320950.2442
26.25770.92230.55182.14233.80028.2153-0.0704-0.2541-1.17940.4477-0.1461.1771.0301-0.83520.11940.6703-0.15120.12830.84530.14980.78758.92960.809466.1291
32.06870.70380.48479.1273.11064.6446-0.0768-0.3767-0.28460.60930.08660.26350.6392-0.40640.02460.5549-0.07120.16940.53940.07740.500817.58146.384567.8592
40.62740.66480.30981.2917-0.19231.4733-0.0482-0.05630.0030.08770.03070.0921-0.1491-0.10220.00140.46530.02320.08020.40270.01740.38325.647217.775456.3231
55.35851.28720.19523.22691.8893.2354-0.1085-0.31840.4716-0.4108-0.02260.4641-0.3894-0.90960.08220.51-0.02590.00560.89050.01680.8206-1.621615.640149.9913
61.77111.31790.15364.17451.31133.65750.8735-0.2461-0.22490.9133-0.67450.1001-0.2991-0.64690.0450.9770.05060.17380.89340.06060.767111.173230.520360.0452
74.4962-1.6835-1.99373.16761.65822.5049-0.05070.2101-0.3279-0.3757-0.03370.31780.3578-0.41220.13770.5522-0.1349-0.02650.49040.03350.470411.92766.525543.9235
83.3633-0.40660.32173.8237-1.034.31190.04010.2846-0.02130.0357-0.02410.491-0.1054-0.45920.0040.52080.00270.11310.4468-0.0690.42819.683210.911733.7994
91.4632-0.21090.74952.6575-0.15811.4775-0.0739-0.15620.12770.19540.04540.2764-0.1961-0.2450.01480.39120.04050.07540.4237-0.01230.379518.951352.681749.8498
102.3544-0.89752.17298.2672-2.14443.2220.088-0.71860.38570.83570.29790.6678-0.5834-0.8046-0.32590.81990.13560.20580.7789-0.07070.511814.335461.633264.2722
110.82770.2415-0.4071.56550.10621.5833-0.0655-0.01260.0956-0.03630.04120.1331-0.1539-0.10210.0280.45520.05350.01190.3955-0.02060.415724.744758.165841.8335
125.23570.913-3.12982.6716-2.65855.842-0.11630.60490.3301-0.21990.26060.79290.2363-0.8812-0.32340.4758-0.0020.03870.89970.00920.8235-1.77950.035443.78
131.7811-0.40860.87962.2507-0.09382.65250.10530.12080.1328-0.2105-0.14340.3938-0.1727-0.29750.01870.60010.0340.11490.5457-0.01850.574311.622350.029343.1825
143.56691.38051.30095.02421.76484.96810.0038-0.2188-0.1699-0.2312-0.06040.5095-0.1332-0.61710.04650.44730.10990.04480.41820.08530.429519.857633.405248.5284
151.65840.690.15771.00490.20483.3806-0.07820.20450.2179-0.19510.04410.3101-0.285-0.2860.03140.3970.0609-0.0320.36850.03760.439517.902951.42882.6257
160.9821-0.40140.02551.7996-0.03842.0855-0.05210.0059-0.0559-0.0750.03250.25240.0728-0.26860.03110.3981-0.0093-0.02730.40770.01290.410121.046641.52124.3335
170.51640.37730.98041.31340.04091.57830.23210.4763-0.1522-0.5491-0.19240.03350.327-0.5936-0.07860.85420.0179-0.06560.98380.00570.78248.632631.84310.6083
181.0242-0.85040.51523.2652-1.59194.84890.1419-0.3018-0.00070.09380.02640.4095-0.0427-0.4406-0.21350.42460.02790.01910.4151-0.06050.41318.868950.792923.3185
191.28380.3099-0.50822.76380.02571.0691-0.05140.1812-0.0536-0.18740.06940.13840.1093-0.1672-0.00980.4173-0.0126-0.02730.4365-0.01290.393120.58439.0759.9684
202.4847-0.13760.9264.2781-1.22995.2216-0.14760.9176-0.3284-0.98090.06670.83610.4987-1.1610.0750.6635-0.1383-0.10590.8003-0.120.75348.9397-7.16771.8986
212.07920.19420.5123.498-0.95695.8443-0.10560.3211-0.2508-0.47480.00850.34260.3952-0.25530.07260.5261-0.1079-0.0210.5344-0.08960.569917.5656-8.62696.7714
220.5745-0.47970.09811.7126-0.08781.6772-0.04440.0038-0.05490.079-0.02650.13790.1297-0.05480.06080.4538-0.04530.03490.4117-0.02060.443425.64582.94818.1373
239.8467-3.24431.99694.4603-3.68655.7786-0.4749-0.76060.00690.59330.56960.9918-0.3138-1.0538-0.07210.5019-0.01550.02030.92020.01790.9209-1.60069.258715.9071
243.1081-1.21143.97056.2891-0.12755.48361.0480.2249-0.58490.3599-0.18290.81251.00560.1772-0.49070.9569-0.16210.05940.9103-0.04130.868911.1837-0.797230.827
255.32431.4843-2.14312.2502-1.09063.24550.11270.34250.1567-0.2922-0.02680.3569-0.3653-0.4213-0.03030.53890.0587-0.11170.4726-0.02670.509111.935515.37496.8941
263.8256-1.2331-0.40964.71632.08114.8871-0.05070.13970.13170.2198-0.04230.58060.0525-0.55180.06740.4613-0.0920.03440.36270.09920.44620.254225.07810.8899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 204 )
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 361 )
5X-RAY DIFFRACTION5chain 'A' and (resid 362 through 382 )
6X-RAY DIFFRACTION6chain 'A' and (resid 383 through 413 )
7X-RAY DIFFRACTION7chain 'A' and (resid 414 through 441 )
8X-RAY DIFFRACTION8chain 'A' and (resid 442 through 482 )
9X-RAY DIFFRACTION9chain 'B' and (resid 0 through 86 )
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 217 )
11X-RAY DIFFRACTION11chain 'B' and (resid 218 through 361 )
12X-RAY DIFFRACTION12chain 'B' and (resid 362 through 382 )
13X-RAY DIFFRACTION13chain 'B' and (resid 383 through 441 )
14X-RAY DIFFRACTION14chain 'B' and (resid 442 through 481 )
15X-RAY DIFFRACTION15chain 'C' and (resid 0 through 235 )
16X-RAY DIFFRACTION16chain 'C' and (resid 236 through 382 )
17X-RAY DIFFRACTION17chain 'C' and (resid 383 through 422 )
18X-RAY DIFFRACTION18chain 'C' and (resid 423 through 481 )
19X-RAY DIFFRACTION19chain 'D' and (resid 0 through 74 )
20X-RAY DIFFRACTION20chain 'D' and (resid 75 through 204 )
21X-RAY DIFFRACTION21chain 'D' and (resid 205 through 235 )
22X-RAY DIFFRACTION22chain 'D' and (resid 236 through 361 )
23X-RAY DIFFRACTION23chain 'D' and (resid 362 through 382 )
24X-RAY DIFFRACTION24chain 'D' and (resid 383 through 413 )
25X-RAY DIFFRACTION25chain 'D' and (resid 414 through 441 )
26X-RAY DIFFRACTION26chain 'D' and (resid 442 through 481 )

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