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- PDB-3okr: Structure of Mtb apo 2-C-methyl-D-erythritol 4-phosphate cytidylt... -

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Basic information

Entry
Database: PDB / ID: 3okr
TitleStructure of Mtb apo 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD)
Components
  • 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
  • Heptamer peptide
KeywordsTRANSFERASE / TB Structural Genomics Consortium / TBSGC / Tryptophan synthesis / IspD / 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase / Mycobacterium tuberculosis / Mtb / TB
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 involved in terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / CTP binding / manganese ion binding / magnesium ion binding / zinc ion binding / plasma membrane
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. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSacchettini, J.C. / Reddy, M.C.M. / Bruning, J.B. / Thurman, C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure of the Mycobacterium tuberculosis 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD): an antitubercular drug target
Authors: Sacchettini, J.C. / Reddy, M.C.M. / Bruning, J.B. / Thurman, C.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Sep 6, 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

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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
F: Heptamer peptide


Theoretical massNumber of molelcules
Total (without water)96,9965
Polymers96,9965
Non-polymers00
Water82946
1
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)48,1912
Polymers48,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-20 kcal/mol
Surface area17490 Å2
MethodPISA
2
C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
F: Heptamer peptide


Theoretical massNumber of molelcules
Total (without water)48,8053
Polymers48,8053
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-20 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.081, 60.268, 74.512
Angle α, β, γ (deg.)104.18, 110.52, 88.68
Int Tables number1
Space group name H-MP1

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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: 24095.439 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ispD, Rv3582c, MT3688, MTCY06G11.29c / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96864, UniProt: P9WKG9*PLUS, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Protein/peptide Heptamer peptide


Mass: 613.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ispD, Rv3582c, MT3688, MTCY06G11.29c / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE AUTHOR STATES THAT CHAIN F IS PART OF THE PROTEIN POLYMER AND IT IS FOUND BETWEEN THE STRUCTURE ...THE AUTHOR STATES THAT CHAIN F IS PART OF THE PROTEIN POLYMER AND IT IS FOUND BETWEEN THE STRUCTURE AND THE SYMMETRY MATE. AS THE DENSITY CONNECTING THE FRAGMENT TO THE ENZYME IS DISORDERED AND LACKING, IT WAS NOT POSSIBLE TO ACCURATELY ASSIGN THE SIDE CHAINS AND IDENTIFY THE PEPTIDES SO THESE RESIDUES WERE MODELED AS ALA. SINCE THE SEQUENCE ALIGNMENT IS UNKNOWN, THE RESIDUES IN CHAIN F WERE CHANGED TO UNK IN THIS ENTRY.

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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: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.056 M Sodium phosphate monobasic monohydrate 1.344 M Potassium phosphate dibasic (pH 8.2), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2009
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.4→41 Å / Num. obs: 33622 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.348 / % possible all: 94.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H3M

1h3m


Resolution: 2.4→25.055 Å / SU ML: 0.38 / σ(F): 1.97 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 1659 5.01 %RANDOM
Rwork0.2098 ---
all0.2133 33132 --
obs0.2133 33132 95.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.673 Å2 / ksol: 0.289 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8499 Å2-2.6432 Å2-1.7935 Å2
2--0.9844 Å21.2725 Å2
3----0.1345 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5725 0 0 46 5771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095791
X-RAY DIFFRACTIONf_angle_d1.2577945
X-RAY DIFFRACTIONf_dihedral_angle_d15.2661965
X-RAY DIFFRACTIONf_chiral_restr0.0761041
X-RAY DIFFRACTIONf_plane_restr0.0051036
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4-2.47060.37231440.28822566271094
2.4706-2.55030.38441230.28482626274995
2.5503-2.64130.33741310.27172585271695
2.6413-2.74690.32171280.24462609273796
2.7469-2.87180.31151440.25162621276596
2.8718-3.0230.32071370.23192601273896
3.023-3.2120.28691340.22862649278396
3.212-3.45940.33521430.21862638278197
3.4594-3.80650.30981350.20762654278996
3.8065-4.35480.25661330.18942663279697
4.3548-5.47710.22031490.16252665281498
5.4771-25.05650.24111580.19562596275496
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)
11.60130.68161.23463.1466-0.05867.63720.2623-0.0256-0.5546-0.4226-0.6619-0.39860.55050.05630.31970.57560.0353-0.01350.47590.04370.5058.5224-19.8521-12.1233
22.6119-1.6798-0.86583.0039-0.59051.7307-0.5422-0.0027-0.51820.7383-0.151-0.4184-0.29060.96170.60180.63010.02930.03910.40580.08580.61244.7633-21.22443.422
32.2203-1.22470.83271.535-0.34293.50230.11110.2841-0.48470.197-0.15650.0151.46440.682-0.01220.65770.16470.03330.45790.00640.44928.1142-26.1701-6.8974
49.6935-5.23536.6576.9679-5.87325.8468-0.89751.45951.24680.5371-0.0032-1.614-1.87321.10750.77230.71490.29280.12210.68670.25040.740817.1531-19.0457-14.9414
55.612-1.9783-1.41723.35990.41692.73450.4920.4705-0.0677-0.6352-0.77780.4732-0.3735-0.29180.13660.49720.1233-0.07890.3431-0.12210.3603-0.6942-11.9266-13.9149
61.13210.1549-0.93331.40520.89751.59330.1873-0.02050.2912-0.0605-0.3556-0.0670.0681-0.11360.0850.48180.03690.02840.29990.05430.36427.7157-0.0243-12.0668
71.9992-2.1285-1.6861.88221.55311.4784-0.2305-0.0849-0.18860.22210.16030.228-0.46380.27370.02390.460.0126-0.06010.40140.05070.45660.2129-8.7441-2.4728
84.26380.9256-1.44116.14431.29381.8325-0.19770.125-0.96091.0354-0.16690.7910.7614-0.33990.2360.5963-0.04980.13490.251-0.06280.4683-13.50369.554613.648
91.5821-0.2366-1.10765.60462.20521.8047-0.2751-0.29660.29991.2936-0.25051.25590.52670.03090.52670.6176-0.02410.16580.3072-0.03910.496-13.706413.036218.0241
104.4227-0.5182-0.51974.5631-4.46117.33360.39160.76580.13640.2291-0.37440.4923-2.02010.01860.29990.4420.03530.08810.4128-0.13670.5752-17.374420.15958.0292
111.9006-1.705-1.76624.19170.00972.3508-0.2671-0.3160.32680.59610.377-0.33580.12830.3129-0.09650.41850.0056-0.14470.3557-0.08150.4216-1.442617.465611.8146
121.0553-0.8576-0.84961.67532.30322.50410.2410.13790.2318-0.3879-0.0336-0.1003-0.04280.2322-0.13650.494-0.0235-0.03550.29830.04930.46851.268312.3982-3.3858
131.99427.81575.72396.05946.33898.46961.21671.4235-2.55381.4359-0.2636-0.52940.4006-1.9004-0.19580.26650.07710.18310.61630.00850.2553-4.504521.4408-1.3129
140.6745-0.9277-1.17913.50192.24081.5698-0.29160.0083-0.16670.66740.034-0.0050.24060.27950.21390.38970.00540.03220.37370.11620.4625-3.06133.95037.7321
152.74-2.8455-1.87292.98322.15673.4842-0.50940.356-0.73050.0993-0.56941.3196-0.1051-1.04870.72350.3160.0825-0.03840.712-0.19240.6562-5.4101-2.335541.8942
165.1417-5.35363.21597.055-1.59354.1164-0.9033-0.1278-0.8927-0.8727-0.34710.3962-1.8438-2.07011.43310.58190.3095-0.25030.6875-0.0751.1359-10.62987.32439.5158
177.50231.18193.10318.8064-3.48433.44770.04970.32880.81440.92051.7833-0.1065-0.07890.5927-1.74210.69930.422-0.46050.8434-0.32151.3554-0.978112.527450.1544
183.0907-2.14220.83293.23270.30250.9275-0.4856-0.7546-0.11450.65360.22610.1108-0.18840.0210.22010.49020.03960.00430.46090.01650.13335.5272-5.398649.6994
192.09020.39850.32842.72692.2352.29240.6852-0.89770.53520.9209-0.26010.0581-0.44830.2518-0.30650.5405-0.15720.12730.489-0.09930.316327.5057-4.119430.4428
203.2743-0.92971.12541.60051.1112.6175-0.9663-0.08790.25890.36320.4835-0.294-0.24540.03860.23090.44380.1471-0.12150.5333-0.08150.369111.59672.633447.949
212.0637-2.9594-2.16784.07413.10622.703-0.0396-0.0135-0.87860.1478-0.190.4572-0.0345-0.43040.29640.4119-0.08670.04020.2963-0.00150.37816.8011-7.495638.3093
225.7738-1.1738-3.42692.98760.30463.8315-0.65120.8446-1.4627-0.21640.08180.99450.4987-1.00890.64830.4598-0.13810.13990.5375-0.09520.764919.9991-26.286320.7693
234.7215-2.5882-1.786.85451.18052.08850.03610.6701-0.8252-0.2751-0.89580.80020.1297-0.36820.71150.4009-0.02280.03710.4324-0.10760.622521.8957-27.817215.7693
243.96210.28891.32252.7631-0.04921.9181-0.14190.42810.07190.38530.1725-1.3623-0.2176-0.132-0.15120.23150.0376-0.04520.2326-0.02910.457334.6397-27.673621.9682
253.73740.7748-0.39954.63981.81872.20530.4624-0.4917-0.1907-0.6034-0.3182-0.4154-0.5025-0.1827-0.17850.43650.01940.07520.34730.09020.306525.6015-11.978917.4285
260.5832-1.07-0.0952.72211.32282.137-0.1832-0.46640.12710.30770.2035-0.4721-0.07930.0585-0.06680.3347-0.0199-0.06030.4251-0.03050.417926.6319-8.386132.8979
275.75824.5093-4.28536.7671-7.40068.302-0.11331.5646-0.08890.75112.0941.6666-0.48350.5665-1.4970.1986-0.01320.13830.6586-0.12390.504933.1384-15.029728.8982
283.6982-1.7105-2.79771.39461.34811.87590.46030.1543-0.12940.2877-0.36730.2994-0.2444-0.20330.02580.3019-0.0496-0.00630.37080.04280.301716.5898-14.348725.4245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:26)
2X-RAY DIFFRACTION2(chain A and resid 27:41)
3X-RAY DIFFRACTION3(chain A and resid 42:77)
4X-RAY DIFFRACTION4(chain A and resid 78:100)
5X-RAY DIFFRACTION5(chain A and resid 101:139)
6X-RAY DIFFRACTION6(chain A and resid 140:198)
7X-RAY DIFFRACTION7(chain A and resid 199:231)
8X-RAY DIFFRACTION8(chain B and resid 7:35)
9X-RAY DIFFRACTION9(chain B and resid 36:74)
10X-RAY DIFFRACTION10(chain B and resid 75:85)
11X-RAY DIFFRACTION11(chain B and resid 86:139)
12X-RAY DIFFRACTION12(chain B and resid 140:179)
13X-RAY DIFFRACTION13(chain B and resid 180:198)
14X-RAY DIFFRACTION14(chain B and resid 199:231)
15X-RAY DIFFRACTION15(chain C and resid 7:57)
16X-RAY DIFFRACTION16(chain C and resid 58:79)
17X-RAY DIFFRACTION17(chain C and resid 87:95)
18X-RAY DIFFRACTION18(chain C and resid 99:138)
19X-RAY DIFFRACTION19(chain C and resid 139:156)
20X-RAY DIFFRACTION20(chain C and resid 157:196)
21X-RAY DIFFRACTION21(chain C and resid 197:231)
22X-RAY DIFFRACTION22(chain D and resid 7:34)
23X-RAY DIFFRACTION23(chain D and resid 35:75)
24X-RAY DIFFRACTION24(chain D and resid 76:98)
25X-RAY DIFFRACTION25(chain D and resid 99:138)
26X-RAY DIFFRACTION26(chain D and resid 139:179)
27X-RAY DIFFRACTION27(chain D and resid 180:197)
28X-RAY DIFFRACTION28(chain D and resid 198:231)

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