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- PDB-4zdq: Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidyly... -

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Basic information

Entry
Database: PDB / ID: 4zdq
TitleCrystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis complexed with CTP
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / SSGCID / isoprenoid biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
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
ACETATE ION / CACODYLIC ACID / CYTIDINE-5'-TRIPHOSPHATE / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Crystal structure and biophysical characterization of IspD from Burkholderia thailandensis and Mycobacterium paratuberculosis.
Authors: Pierce, P.G. / Hartnett, B.E. / Laughlin, T.M. / Blain, J.M. / Mayclin, S.J. / Bolejack, M.J. / Myers, J.B. / Higgins, T.W. / Dranow, D.M. / Sullivan, A. / Lorimer, D.D. / Edwards, T.E. / ...Authors: Pierce, P.G. / Hartnett, B.E. / Laughlin, T.M. / Blain, J.M. / Mayclin, S.J. / Bolejack, M.J. / Myers, J.B. / Higgins, T.W. / Dranow, D.M. / Sullivan, A. / Lorimer, D.D. / Edwards, T.E. / Hagen, T.J. / Horn, J.R. / Myler, P.J.
History
DepositionApr 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Derived calculations
Revision 1.2Oct 11, 2017Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / reflns_shell
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.3Sep 27, 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
Revision 1.4Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)105,12120
Polymers103,2864
Non-polymers1,83516
Water3,369187
1
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6248
Polymers25,8211
Non-polymers8037
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)25,8211
Polymers25,8211
Non-polymers00
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)26,1375
Polymers25,8211
Non-polymers3154
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)26,5396
Polymers25,8211
Non-polymers7185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4459
Polymers51,6432
Non-polymers8037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-27 kcal/mol
Surface area18120 Å2
MethodPISA
6
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)52,67611
Polymers51,6432
Non-polymers1,0339
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-23 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.900, 138.950, 76.920
Angle α, β, γ (deg.)90.000, 101.940, 90.000
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
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase / MEP cytidylyltransferase / MCT


Mass: 25821.379 Da / Num. of mol.: 4 / Fragment: ButhA.00168.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: ispD, BTH_I2089 / Plasmid: ButhA.00168.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2SWT6, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

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Non-polymers , 6 types, 203 molecules

#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7AsO2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.05
Details: ButhA.00168.a.A1.PW33338 at 30.46 mg/ml mixed 1:1 with JCSG+(e11): 10.73% PEG-8000, 80mM Sodium Cacodylate/ HCl, pH=6.04, 160mM Calcium acetate, 20% glycerol. Apo crystals were soaked with ...Details: ButhA.00168.a.A1.PW33338 at 30.46 mg/ml mixed 1:1 with JCSG+(e11): 10.73% PEG-8000, 80mM Sodium Cacodylate/ HCl, pH=6.04, 160mM Calcium acetate, 20% glycerol. Apo crystals were soaked with 1mM MgCl2, CTP, and D-erythritol-4-phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 41718 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 31.72 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.094 / Χ2: 0.951 / Net I/σ(I): 13.44 / Num. measured all: 159992
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.360.8220.5392.8411811306930580.62699.6
2.36-2.420.8380.4893.0911664303330180.56799.5
2.42-2.490.9120.3873.8411163288828900.449100
2.49-2.570.930.3274.4211044287528590.3899.4
2.57-2.660.9370.2894.8810634274427480.335100
2.66-2.750.9530.2495.6510146264426300.28999.5
2.75-2.850.9670.26.799964257825820.233100
2.85-2.970.9790.1578.589532248224720.18399.6
2.97-3.10.9890.119119138238823770.13899.5
3.1-3.250.9910.09313.668737226622710.108100
3.25-3.430.9950.06917.678208214321360.0899.7
3.43-3.640.9960.05820.557755204920440.06899.8
3.64-3.890.9970.04824.067359193819360.05699.9
3.89-4.20.9970.04227.296848180618000.04899.7
4.2-4.60.9980.03531.116327165616560.04100
4.6-5.140.9980.03332.295680149114880.03999.8
5.14-5.940.9980.03828.244999131113100.04499.9
5.94-7.270.9980.03330.344231111311120.03999.9
7.27-10.290.9980.02737.5232038688660.03299.8
10.290.9980.03135.6515494924650.03794.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4YS8

4ys8


Resolution: 2.3→26.932 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 1948 4.67 %
Rwork0.205 39739 -
obs0.2074 41687 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.49 Å2 / Biso mean: 41.7333 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: final / Resolution: 2.3→26.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 111 187 6950
Biso mean--63.4 37.2 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026892
X-RAY DIFFRACTIONf_angle_d0.5639376
X-RAY DIFFRACTIONf_chiral_restr0.0281075
X-RAY DIFFRACTIONf_plane_restr0.0031240
X-RAY DIFFRACTIONf_dihedral_angle_d10.0672431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.3241420.27292794293699
2.3575-2.42120.28611390.258628572996100
2.4212-2.49240.31441100.243828162926100
2.4924-2.57280.29211450.240928633008100
2.5728-2.66470.27971410.241328092950100
2.6647-2.77120.30961440.2428352979100
2.7712-2.89720.30131490.236128132962100
2.8972-3.04980.29641430.23928593002100
3.0498-3.24060.30351290.22128572986100
3.2406-3.49030.26631280.208728422970100
3.4903-3.84060.22491470.189128512998100
3.8406-4.39430.21511370.172328062943100
4.3943-5.52850.20541370.162828753012100
5.5285-26.93350.24061570.1832862301999
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)
13.5476-0.7945-0.06134.21770.22782.3539-0.09980.0255-0.2748-0.1377-0.0022-0.310.15190.16560.12240.1477-0.01180.04870.2385-0.00990.265146.592589.729543.5234
20.67210.1795-0.18214.20850.0560.7020.1243-0.07680.08340.2773-0.08160.7878-0.03990.0564-0.02280.1934-0.0340.06180.2551-0.06580.297530.662482.594847.245
32.1093-0.7632-0.65015.56071.98443.47570.0546-0.0321-0.28890.21450.00940.16290.15350.1995-0.10180.1927-0.05520.0180.2771-0.01740.281435.694579.175646.118
41.83180.9959-0.17323.47220.45342.3593-0.1150.1056-0.0046-0.08020.07520.1307-0.1851-0.0670.03290.32130.0248-0.04920.2359-0.01260.196331.444748.098836.1317
50.8390.8679-0.45586.74710.37540.62680.0374-0.02870.0970.3021-0.07940.46610.1659-0.06670.00580.3223-0.0039-0.00470.2788-0.02720.264628.298560.794846.6621
65.00830.2466-0.75223.04621.82333.8215-0.0249-0.53930.180.34680.1588-0.4115-0.62260.3447-0.21680.46980.0401-0.05290.2423-0.00010.211228.1215116.75490.1197
72.14220.89070.39655.48361.07845.96910.10050.3419-0.3062-0.25890.12380.5220.59230.2228-0.28890.33130.0267-0.1420.3576-0.03520.291720.7855102.4349-11.815
85.19050.21381.38964.2171-1.82261.2736-0.11170.31240.2677-0.13880.1755-0.07020.1560.05740.00210.23590.035-0.0610.1866-0.00940.147724.5301112.448-10.9135
92.92961.21391.20933.3021-0.58054.1719-0.24710.2353-0.1468-0.39170.1523-0.17880.24130.07630.09920.26850.037-0.05020.28720.00720.200123.9021112.9246-14.1606
100.526-0.8898-1.40671.54832.41783.79580.27820.6716-0.5856-0.4626-0.2561-0.1801-0.71610.375-0.03680.3668-0.012-0.07060.36150.01890.57435.0914116.2704-8.3764
113.58690.09460.54363.1108-1.75913.27890.0595-0.44180.32570.7838-0.0474-0.4063-0.1166-0.00460.00640.3330.0451-0.06940.2765-0.01120.260928.5088108.3844.2667
125.57820.80881.55468.8141.54930.6349-0.40.08710.454-0.54060.0671-0.9089-0.9119-0.18580.12120.39910.0903-0.07390.29210.08930.459841.284481.3560.7951
134.6474-4.179-1.41993.75811.28280.4763-0.3999-0.5558-0.20430.47020.3187-0.1773-0.22950.24150.01110.43550.0107-0.17930.26970.01890.427338.735589.51136.6101
143.65060.05941.54818.1207-0.46486.3978-0.13170.33090.21180.14740.0788-1.0037-0.49120.50550.09360.283-0.027-0.13090.22760.04740.427740.4194113.822-0.3517
153.2570.81453.63849.2002-1.02576.08950.19160.43790.004-0.0975-0.0325-1.6710.22220.906-0.17280.36280.0769-0.16750.42260.02850.71444.3659106.97321.2236
166.21461.65323.25297.71232.42438.0717-0.1145-0.4513-0.3013-0.2818-0.05840.1153-0.5755-0.35020.14860.31060.0626-0.11150.19150.04240.328927.845896.87851.852
177.58121.4423-2.50179.3959-0.19713.76030.6910.5659-0.8931-0.76070.24751.02330.2104-0.6495-0.74230.71540.0272-0.2740.38120.10030.591219.210390.6738-7.599
184.7572-1.2587-0.93986.18140.0174.23020.2709-0.1440.4740.00620.0370.68960.0597-0.4337-0.19430.2177-0.06370.02890.3175-0.00580.343118.499869.18347.1175
195.8762-0.456-0.72164.3446-0.01742.6874-0.2248-0.56820.06690.69730.0980.64210.2116-0.22050.0260.34920.00010.02850.28530.01530.300221.605464.108712.32
201.48951.13550.42336.3723-0.31161.0563-0.25070.01630.0405-0.35620.2315-0.4589-0.06280.09080.02770.28030.0198-0.04720.28840.02790.235334.452579.31351.4788
215.118-1.33070.75644.878-0.40832.1611-0.0941-0.3184-0.05670.17880.0413-0.1521-0.04910.01030.02350.2487-0.0215-0.05070.27610.06920.371432.500874.87796.7112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 96 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 185 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 231 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 138 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 139 through 232 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 11 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 12 through 43 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 44 through 63 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 64 through 81 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 82 through 96 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 97 through 138 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 139 through 152 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 153 through 168 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 169 through 185 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 186 through 204 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 205 through 218 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 219 through 232 )C0
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 63 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 64 through 96 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 97 through 168 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 169 through 230 )D0

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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