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- PDB-3q80: Structure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltrans... -

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Basic information

Entry
Database: PDB / ID: 3q80
TitleStructure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD) Complexed with CDP-ME
Components2-C-methyl-D-erythritol 4-phosphate cytidyltransferase
KeywordsTRANSFERASE / TB Structural Genomics Consortium / TBSGC / Rossmann fold / 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase
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
4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL / 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 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 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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)49,36010
Polymers48,1272
Non-polymers1,2338
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-98 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.581, 92.668, 146.421
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-CDM / 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL


Mass: 521.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25N3O14P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris 8.5, 25% PEG 3350, 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 11, 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→50 Å / Num. all: 36096 / Num. obs: 36096 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 34.26 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Χ2: 1.997 / Net I/σ(I): 31.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2-2.072.20.2634.2423540.2631.47460.5
2.07-2.152.60.1996.3928110.2631.55473.3
2.15-2.253.30.14710.4634020.1471.81388
2.25-2.374.40.12414.2138690.1241.76499.6
2.37-2.524.50.09818.7938900.0981.89399.9
2.52-2.714.50.07624.7839170.0762.03499.8
2.71-2.994.60.06131.1639300.0612.19799.8
2.99-3.424.70.05435.9839070.0542.35199.4
3.42-4.314.70.04837.3939370.0482.20298.4
4.31-504.60.04636.6740790.0461.85596.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1i52


Resolution: 2→24.796 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.8646 / SU ML: 0.21 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 1806 5.01 %random
Rwork0.1651 ---
all0.167 36029 --
obs0.167 36029 91.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.533 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 123.73 Å2 / Biso mean: 38.6502 Å2 / Biso min: 13.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.2307 Å20 Å20 Å2
2--0.053 Å20 Å2
3---0.1777 Å2
Refinement stepCycle: LAST / Resolution: 2→24.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3197 0 72 357 3626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073351
X-RAY DIFFRACTIONf_angle_d1.1264610
X-RAY DIFFRACTIONf_chiral_restr0.069575
X-RAY DIFFRACTIONf_plane_restr0.004592
X-RAY DIFFRACTIONf_dihedral_angle_d19.4011287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2-2.05210.286770.215616571734173458
2.0521-2.11250.26881080.196319522060206069
2.1125-2.18060.23971180.186822442362236279
2.1806-2.25850.2231430.163725572700270091
2.2585-2.34880.23131710.163281629872987100
2.3488-2.45570.20721360.1544285029862986100
2.4557-2.5850.22841430.1587285329962996100
2.585-2.74680.19671460.1738284429902990100
2.7468-2.95850.22881280.1792287530033003100
2.9585-3.25570.23281490.183628563005300599
3.2557-3.72540.19251410.169128703011301199
3.7254-4.68840.16651770.142528673044304498
4.6884-24.7980.18791690.161229823151315197
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)
11.6645-0.18550.64432.16940.36390.533-0.0287-0.1484-0.00470.11290.0434-0.1890.0505-0.0269-0.0220.21470.00630.02840.24880.01750.213612.7624-31.111127.1983
21.00990.2195-0.43460.56340.14930.5810.0564-0.0296-0.1012-0.0976-0.1035-0.4468-0.05160.3023-0.00520.27110.0360.07950.27320.01250.330918.4833-35.644921.166
32.0259-0.70590.47840.6141-0.48331.12590.0694-0.0274-0.2654-0.2681-0.06940.12450.2591-0.1062-0.03140.3308-0.0184-0.01730.2402-0.010.2619-0.5973-35.699419.1746
40.4098-0.4749-0.23581.459-0.16831.00830.14380.0353-0.0701-0.561-0.00710.11360.0378-0.0335-0.09690.33810.002-0.01950.2114-0.03090.1664-0.6936-21.062710.6848
51.7978-0.33710.8571.8617-0.10820.62150.05820.15-0.0388-0.627-0.10250.04920.0771-0.02780.02640.41850.00560.00220.2464-0.01520.21364.6513-28.623413.0044
64.81854.7185-4.35544.6202-4.26573.9381-0.0694-1.5758-0.13231.3471-0.64650.015-0.56020.91260.60460.3245-0.0256-0.02640.41830.01040.22652.4985-21.348137.3151
70.756-0.5565-0.09962.03050.41430.7005-0.0766-0.20980.13420.12550.1670.2215-0.0691-0.0385-0.08220.15390.0074-0.02030.2633-0.02770.2084-12.8712-3.190130.2029
80.8728-0.9745-0.30632.17690.7941.23990.0344-0.00460.0515-0.2082-0.07320.2455-0.2411-0.14870.05640.16530.0141-0.04990.1566-0.00830.2017-16.62921.573624.4806
95.75752.4886-5.01064.2411-2.01347.99410.2675-0.42990.7602-0.4218-0.4102-1.0281-0.66640.98710.0770.4003-0.07940.06260.3592-0.01830.48191.19847.682915.7477
100.73550.01120.20761.39320.0761.10760.09660.11420.1231-0.65520.0104-0.0721-0.10550.0203-0.07930.38060.008-0.01650.25960.0270.2053-5.7766-9.483910.5965
110.7239-0.454-0.44911.48240.28040.43460.0396-0.06180.044-0.4531-0.0825-0.00840.0423-0.03530.01360.322-0.0075-0.02580.26410.0180.2038-6.9512-6.557415.0889
127.35270.2196-2.14875.1681-0.76510.7764-0.0373-0.90580.11390.41650.14770.30440.18740.0647-0.07550.28230.02030.02080.31190.020.2235-3.6488-12.935436.6146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:63)A6 - 63
2X-RAY DIFFRACTION2(chain A and resid 64:95)A64 - 95
3X-RAY DIFFRACTION3(chain A and resid 100:138)A100 - 138
4X-RAY DIFFRACTION4(chain A and resid 139:175)A139 - 175
5X-RAY DIFFRACTION5(chain A and resid 176:222)A176 - 222
6X-RAY DIFFRACTION6(chain A and resid 223:231)A223 - 231
7X-RAY DIFFRACTION7(chain B and resid 6:53)B6 - 53
8X-RAY DIFFRACTION8(chain B and resid 54:119)B54 - 119
9X-RAY DIFFRACTION9(chain B and resid 120:129)B120 - 129
10X-RAY DIFFRACTION10(chain B and resid 130:186)B130 - 186
11X-RAY DIFFRACTION11(chain B and resid 187:220)B187 - 220
12X-RAY DIFFRACTION12(chain B and resid 221:231)B221 - 231

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