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- PDB-7kmw: Crystal structure of IspD from Mycobacterium paratuberculosis -

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Basic information

Entry
Database: PDB / ID: 7kmw
TitleCrystal structure of IspD from Mycobacterium paratuberculosis
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / IspD / cytidylyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process
Similarity search - Function
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesMycolicibacterium paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of IspD from Mycobacterium paratuberculosis
Authors: Pierce, P.G. / Bolejack, M.J. / Yano, J.K. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Other / Structure summary
Category: audit_author / pdbx_SG_project ...audit_author / pdbx_SG_project / pdbx_database_status / struct_keywords
Item: _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,64516
Polymers104,9004
Non-polymers74512
Water4,107228
1
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4735
Polymers26,2251
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2872
Polymers26,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4735
Polymers26,2251
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4114
Polymers26,2251
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.130, 45.620, 121.560
Angle α, β, γ (deg.)90.000, 126.750, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 37 through 46 or resid 58...
21(chain B and (resid 37 through 46 or resid 58...
31(chain C and (resid 37 through 79 or resid 83...
41(chain D and (resid 37 through 46 or resid 58...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 37 through 46 or resid 58...A37 - 46
121(chain A and (resid 37 through 46 or resid 58...A58 - 79
131(chain A and (resid 37 through 46 or resid 58...A83 - 91
141(chain A and (resid 37 through 46 or resid 58...A92 - 93
151(chain A and (resid 37 through 46 or resid 58...A29 - 257
161(chain A and (resid 37 through 46 or resid 58...A29 - 257
171(chain A and (resid 37 through 46 or resid 58...A29 - 257
181(chain A and (resid 37 through 46 or resid 58...A29 - 257
211(chain B and (resid 37 through 46 or resid 58...B37 - 46
221(chain B and (resid 37 through 46 or resid 58...B58 - 79
231(chain B and (resid 37 through 46 or resid 58...B83 - 91
241(chain B and (resid 37 through 46 or resid 58...B92 - 93
251(chain B and (resid 37 through 46 or resid 58...B35 - 257
261(chain B and (resid 37 through 46 or resid 58...B35 - 257
271(chain B and (resid 37 through 46 or resid 58...B35 - 257
281(chain B and (resid 37 through 46 or resid 58...B35 - 257
311(chain C and (resid 37 through 79 or resid 83...C37 - 79
321(chain C and (resid 37 through 79 or resid 83...C83 - 91
331(chain C and (resid 37 through 79 or resid 83...C92 - 93
341(chain C and (resid 37 through 79 or resid 83...C37 - 257
351(chain C and (resid 37 through 79 or resid 83...C37 - 257
361(chain C and (resid 37 through 79 or resid 83...C37 - 257
371(chain C and (resid 37 through 79 or resid 83...C37 - 257
411(chain D and (resid 37 through 46 or resid 58...D37 - 46
421(chain D and (resid 37 through 46 or resid 58...D58 - 61
431(chain D and (resid 37 through 46 or resid 58...D62
441(chain D and (resid 37 through 46 or resid 58...D34 - 401
451(chain D and (resid 37 through 46 or resid 58...D34 - 401
461(chain D and (resid 37 through 46 or resid 58...D34 - 401
471(chain D and (resid 37 through 46 or resid 58...D34 - 401

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Components

#1: Protein
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase / MEP cytidylyltransferase / MCT


Mass: 26224.928 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10) (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: ispD, MAP_0476 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q743W5, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein at 17.55 mg/ml with 7 mM each MgCl2 and HGN-0372 was combined 1:1 with 0.2 M MgCl2, 0.1 M Bis-Tris: HCl, pH 6.5, and 25% (w/v) PEG 3350 (MCSG-1 B4). Puck gkq9-5. Harvested with 15% EG.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 7, 2017
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→43.78 Å / Num. obs: 36103 / % possible obs: 99.4 % / Redundancy: 4.1725 % / CC1/2: 0.996 / Net I/σ(I): 9.85
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 4.229 % / Mean I/σ(I) obs: 2.13 / Num. unique obs: 2679 / CC1/2: 0.882 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc2-4022refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q80

3q80


Resolution: 2.35→43.78 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 2013 6.04 %
Rwork0.1801 31334 -
obs0.1827 33347 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.45 Å2 / Biso mean: 50.3249 Å2 / Biso min: 22.35 Å2
Refinement stepCycle: final / Resolution: 2.35→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 48 229 6281
Biso mean--52.23 46.1 -
Num. residues----856
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3461X-RAY DIFFRACTION13.699TORSIONAL
12B3461X-RAY DIFFRACTION13.699TORSIONAL
13C3461X-RAY DIFFRACTION13.699TORSIONAL
14D3461X-RAY DIFFRACTION13.699TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.410.36281350.2931965210081
2.41-2.470.29491350.26291952208783
2.47-2.550.31431340.24892043217785
2.55-2.630.3351340.24132054218886
2.63-2.720.27661440.23452131227589
2.72-2.830.3191340.22662170230490
2.83-2.960.25811690.20612216238593
2.96-3.120.27531510.20032317246895
3.12-3.310.2271280.19012321244996
3.31-3.570.24561280.17492372250098
3.57-3.930.20971370.16812421255898
3.93-4.490.19811600.14822423258399
4.49-5.660.1671530.14712437259099
5.66-43.780.16641710.15092512268399
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)
17.65940.42341.25314.51231.25263.76210.0080.0037-0.19140.11690.1498-0.47620.14430.1524-0.12920.28520.01090.02750.1692-0.01650.2232-15.2289-16.01921.9938
24.9370.8414-3.88820.43910.18158.46170.1290.07210.13850.2018-0.28640.2904-0.0775-0.62380.1250.328-0.0282-0.00110.2704-0.06380.4508-31.9359-10.353916.1824
38.6654-1.93521.14973.71384.77058.03680.0537-0.6781-0.47930.39940.06190.1463-0.15130.1301-0.14840.3696-0.033-0.0150.27710.04370.31-14.2128-8.454713.4215
44.15021.91170.72036.22051.32293.7266-0.0083-0.1278-0.70190.0998-0.0702-0.00770.627-0.62640.0150.3716-0.08950.01460.32340.04570.393-30.3044-20.71215.4108
57.611-1.8943-0.08754.4142-1.13026.50810.10750.06340.4305-0.69160.07380.7994-0.0367-0.1791-0.10120.4096-0.03040.0470.31250.02830.4177-34.71367.429736.6341
64.7283-1.32835.12410.4166-1.23586.4033-0.0977-1.0904-1.41360.42690.3183-0.81060.96711.7762-0.40550.6490.0720.0141.2791-0.10460.5185-15.6257-2.062852.917
76.65360.3324-1.1042.20120.9355.7392-0.4974-1.2728-0.5690.45580.5381-0.33920.49290.6871-0.04920.47960.13660.05780.7259-0.02060.4036-24.61854.249650.5708
85.1733-1.6896-1.37622.5378-1.80552.9212-0.2302-0.7263-0.50330.44090.6951-0.07620.88240.8437-0.25930.61050.11120.05340.50040.01640.3573-28.92420.821948.2035
96.1344-0.372-1.41891.96850.51816.0709-0.0253-0.30750.49570.05590.0764-0.10.27220.3868-0.11340.33890.00280.02330.2806-0.11630.2454-25.37527.221738.8357
109.456-5.6731-3.57755.51063.03752.0310.3418-0.50060.6592-0.21180.1393-0.552-0.29960.4043-0.40220.3099-0.0766-0.00980.42830.01710.2161-9.01860.043426.2248
114.98170.5764-1.97817.17774.11479.59230.12450.0571-0.0812-0.58530.14640.83650.0899-0.3997-0.06440.2907-0.0324-0.02690.31150.02160.3408-30.33571.551129.7194
127.562-0.6823-1.16544.75784.80914.9534-0.0586-0.4549-1.481-0.07320.17330.02420.96660.6221-0.36050.42790.0499-0.01040.44770.03440.4495-23.8169-4.310428.3076
135.057-0.68863.01193.31190.41855.4580.1854-1.0169-0.04840.33870.5324-0.48350.12171.0002-0.48730.29150.0377-0.00050.9793-0.19460.4936-9.38374.227541.5574
143.45731.4561-1.24735.23551.10428.74150.2745-1.29840.88450.0270.1591-0.066-0.7760.3553-0.46260.2247-0.0121-0.020.6886-0.180.470817.70890.756433.533
156.36490.5252-0.80032.72440.57523.1583-0.0643-1.02530.4516-0.00270.0596-0.0451-0.05260.13470.01730.29290.0477-0.06770.48880.00710.286219.2323-3.6530.8808
168.7736-5.49822.14965.0133-1.73381.41540.0699-0.8151-0.218-0.10350.1513-0.0143-0.0842-0.1421-0.25780.2993-0.07940.02580.4863-0.02920.2536-5.1797-5.547126.4456
173.4366-0.7355-1.78292.69042.51838.20120.0869-0.82070.2396-0.01450.1557-0.001-0.3545-0.1068-0.2410.250.0217-0.01220.48780.00480.30317.3361-4.027527.5727
189.5824-1.0580.64492.70850.75322.2182-0.03460.1851-0.5598-0.2003-0.12690.0180.1003-0.18310.12430.3396-0.09150.03810.26110.01930.3592-55.7195-25.862822.8338
193.84182.7688-1.00792.1786-1.19741.4820.0928-0.1796-0.0665-0.0823-0.1852-0.0726-0.1016-0.085-0.01750.33190.03150.01590.3542-0.05610.3407-40.9664-16.676322.0025
203.9375-0.17360.03054.2852-1.10446.0587-0.03260.3453-1.34640.30430.1148-0.38960.9810.3215-0.01640.53440.0165-0.00210.2531-0.03380.6138-15.3258-24.0181-0.184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 101 through 155 )D101 - 155
2X-RAY DIFFRACTION2chain 'D' and (resid 156 through 195 )D156 - 195
3X-RAY DIFFRACTION3chain 'D' and (resid 196 through 226 )D196 - 226
4X-RAY DIFFRACTION4chain 'D' and (resid 227 through 257 )D227 - 257
5X-RAY DIFFRACTION5chain 'A' and (resid 29 through 45 )A29 - 45
6X-RAY DIFFRACTION6chain 'A' and (resid 46 through 67 )A46 - 67
7X-RAY DIFFRACTION7chain 'A' and (resid 68 through 100 )A68 - 100
8X-RAY DIFFRACTION8chain 'A' and (resid 101 through 114 )A101 - 114
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 155 )A115 - 155
10X-RAY DIFFRACTION10chain 'A' and (resid 156 through 195 )A156 - 195
11X-RAY DIFFRACTION11chain 'A' and (resid 196 through 210 )A196 - 210
12X-RAY DIFFRACTION12chain 'A' and (resid 211 through 226 )A211 - 226
13X-RAY DIFFRACTION13chain 'A' and (resid 227 through 257 )A227 - 257
14X-RAY DIFFRACTION14chain 'B' and (resid 35 through 67 )B35 - 67
15X-RAY DIFFRACTION15chain 'B' and (resid 68 through 155 )B68 - 155
16X-RAY DIFFRACTION16chain 'B' and (resid 156 through 195 )B156 - 195
17X-RAY DIFFRACTION17chain 'B' and (resid 196 through 257 )B196 - 257
18X-RAY DIFFRACTION18chain 'C' and (resid 37 through 156 )C37 - 156
19X-RAY DIFFRACTION19chain 'C' and (resid 157 through 257 )C157 - 257
20X-RAY DIFFRACTION20chain 'D' and (resid 34 through 100 )D34 - 100

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