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- PDB-3q7u: Structure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltrans... -

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Basic information

Entry
Database: PDB / ID: 3q7u
TitleStructure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD) complexed with CTP
Components2-C-methyl-D-erythritol 4-phosphate cytidyltransferase
KeywordsTRANSFERASE / TB Structural Genomics Consortium / TBSGC / Rossmann fold / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
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
CYTIDINE-5'-TRIPHOSPHATE / 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 / molecular replacement / Resolution: 2.1 Å
AuthorsReddy, M.C.M. / Bruning, J.B. / Thurman, C. / Ioerger, T.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Proteins / Year: 2011
Title: Crystal Structure of Mycobacterium tuberculosis 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD): a candidate antitubercular drug target
Authors: Reddy, M.C.M. / Bruning, J.B. / Thurman, C. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionJan 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
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_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.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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 cytidyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1426
Polymers48,1272
Non-polymers1,0154
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-39 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.214, 76.756, 131.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24063.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ispD, Rv3582c, MT3688, MTCY06G11.29c / Plasmid: pET28b / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.4M NaH2PO4, 1.6M K2HPO4, 0.1M imidazole, 0.2M NaCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2008 / Details: mirrors
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→42.43 Å / Num. all: 33407 / Num. obs: 33407 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.03 % / Biso Wilson estimate: 36.81 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Χ2: 0.94 / Net I/σ(I): 8.7 / Scaling rejects: 2026
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueΧ2% possible all
2.1-2.188.010.422.72656032752.71.34100
2.18-2.268.030.363.32667632893.31.28100
2.26-2.378.050.3043.82669932883.81.17100
2.37-2.498.070.2784.22699833214.21.1100
2.49-2.658.060.2195.32687033105.30.99100
2.65-2.858.090.1617.42697633047.40.8999.9
2.85-3.148.10.1139.72708833259.70.73100
3.14-3.598.110.09311.627333335211.60.69100
3.59-4.528.060.06516.627529339616.60.63100
4.52-42.437.690.05321.427403354721.40.67100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I52

1i52


Resolution: 2.1→38.378 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8178 / SU ML: 0.3 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 1724 5.16 %random
Rwork0.1882 ---
all0.1906 33397 --
obs0.1906 33397 99.97 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.384 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 111.98 Å2 / Biso mean: 40.1447 Å2 / Biso min: 15.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.0792 Å20 Å20 Å2
2--0.2596 Å20 Å2
3----0.3388 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 60 396 3715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073377
X-RAY DIFFRACTIONf_angle_d1.1454638
X-RAY DIFFRACTIONf_chiral_restr0.071585
X-RAY DIFFRACTIONf_plane_restr0.004599
X-RAY DIFFRACTIONf_dihedral_angle_d20.281266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.1-2.16180.33571480.2856257827262970
2.1618-2.23160.3171280.2616261527432843
2.2316-2.31130.27971540.2354259927532805
2.3113-2.40390.25751400.2339260727472784
2.4039-2.51330.31251230.2218261327362772
2.5133-2.64570.26371460.2221262727732745
2.6457-2.81150.2541330.2093261227452773
2.8115-3.02840.27791570.2048261527722736
3.0284-3.33310.23991650.1961261927842747
3.3331-3.8150.23481370.1797266828052753
3.815-4.8050.17771520.1357269128432743
4.805-38.38440.20231410.1722282929702726
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)
10.3976-0.3191-0.44220.56780.39850.5909-0.03430.0207-0.0108-0.1033-0.0417-0.11830.2928-0.02250.03280.2726-0.0084-0.06710.16360.0190.256918.6363-6.23549.049
21.09150.5910.07711.4403-0.9572.0447-0.01330.137-0.0493-0.1710.0007-0.05530.08520.00840.00910.19530.0304-0.03290.1045-0.00730.168320.83961.80521.9501
30.04990.04880.2882-0.03660.15470.78050.0695-0.00980.1675-0.0816-0.14420.0902-0.2391-0.07860.06770.2358-0.05260.00650.1974-0.02570.265922.038813.32924.8444
42.24460.5177-0.79021.59710.58980.8990.1051-0.3855-0.1339-0.15120.008-0.3055-0.34440.2784-0.07770.2122-0.05650.00860.25820.06890.284631.078113.61595.6209
50.73090.1027-0.31270.43810.12571.3880.1172-0.19650.04980.32-0.24370.07370.05860.04390.08620.2311-0.0005-0.01130.20580.03070.223214.01191.590817.7667
61.38050.3293-0.1611.41961.12052.97070.0472-0.15140.18360.0137-0.03610.09820.0185-0.4561-0.02780.1736-0.0565-0.00640.35420.05340.22888.83995.109246.5441
70.9419-0.1393-0.96591.6126-0.1791.8980.0204-0.1453-0.117-0.14170.1372-0.54310.04570.9893-0.05520.1919-0.012-0.02080.2803-0.01550.243527.77285.290741.5512
80.08030.0526-0.23680.46710.48241.42980.0081-0.17680.0888-0.11390.11440.0937-0.38010.3026-0.12290.2675-0.09250.00490.2078-0.00290.265223.087113.850726.4863
92.08040.04060.13780.53940.17180.4613-0.0834-0.01341.0849-0.3064-0.02750.3917-0.7135-0.47330.09910.320.0065-0.03970.3563-0.04450.421218.717721.002244.6797
100.06880.10770.23150.7058-0.10611.2911-0.0573-0.15670.0953-0.11680.0313-0.02340.1725-0.1689-0.0010.1846-0.07420.00150.1866-0.03120.202614.46630.633133.1718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:47)A6 - 47
2X-RAY DIFFRACTION2(chain A and resid 48:131)A48 - 131
3X-RAY DIFFRACTION3(chain A and resid 132:168)A132 - 168
4X-RAY DIFFRACTION4(chain A and resid 169:201)A169 - 201
5X-RAY DIFFRACTION5(chain A and resid 202:231)A202 - 231
6X-RAY DIFFRACTION6(chain B and resid 6:122)B6 - 122
7X-RAY DIFFRACTION7(chain B and resid 123:139)B123 - 139
8X-RAY DIFFRACTION8(chain B and resid 140:170)B140 - 170
9X-RAY DIFFRACTION9(chain B and resid 171:200)B171 - 200
10X-RAY DIFFRACTION10(chain B and resid 201:231)B201 - 231

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