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- PDB-4dxl: Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythr... -

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Basic information

Entry
Database: PDB / ID: 4dxl
TitleCrystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abscessus, bound to CMP and ATP
Components4-diphosphocytidyl-2-C-methyl-D-erythritol kinase4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
KeywordsTRANSFERASE / SSGCID / NIH / NIAID / SBRI / Emerald BioStructures / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase / 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
4-diphosphocytidyl-2C-methyl-D-erythritol kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup ...4-diphosphocytidyl-2C-methyl-D-erythritol kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-MONOPHOSPHATE / 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
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 / 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 / _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: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6084
Polymers32,7431
Non-polymers8663
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.590, 110.090, 53.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

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Components

#1: Protein 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase / 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase / IspE / CMK / 4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase


Mass: 32742.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: ispE, MAB_1139 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1MKD5, 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Internal tracking number 230819a2, INDEX screen condition A2: 2 M ammonium sulfate, 0.1 M acetate, pH 4.5, MyabA.00725.a.A1 PW30213 at 29.3 mg/mL in 25 mM HEPES, pH 7.0, 500 mM sodium ...Details: Internal tracking number 230819a2, INDEX screen condition A2: 2 M ammonium sulfate, 0.1 M acetate, pH 4.5, MyabA.00725.a.A1 PW30213 at 29.3 mg/mL in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 2 mM CDP, 2 mM ATP, 2 mM meso-erythritol, cryoprotectant: Al's oil, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17719 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 18.285 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.053.50.1926.44551130493.4
2.05-2.110.1667.24535128494.1
2.11-2.170.1677.85015127197.8
2.17-2.240.2416.83845100177.2
2.24-2.310.2497.1180752241.9
2.31-2.390.15210.65419115796
2.39-2.480.107135637113998
2.48-2.580.1145812112298.7
2.58-2.70.09215.45965106398.9
2.7-2.830.08616.86393103799.1
2.83-2.980.07321.2685098999.3
2.98-3.160.06422.8636892299.6
3.16-3.380.05824.5609989199.8
3.38-3.650.0626.3523081497.6
3.65-40.06128.7405766086.6
4-4.470.04531456969298.3
4.47-5.160.04131.2416963199.8
5.16-6.320.04827.23503531100
6.32-8.940.05229.1272443999.8
8.940.0530.8140525096.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PYG

3pyg


Resolution: 2→35.562 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.838 / SU B: 7.914 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 905 5.1 %RANDOM
Rwork0.193 ---
obs0.196 17719 92.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.73 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2→35.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 53 215 2448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192299
X-RAY DIFFRACTIONr_bond_other_d0.0010.021435
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9793161
X-RAY DIFFRACTIONr_angle_other_deg0.92333507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99623.97893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8115309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8481516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212652
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 62 -
Rwork0.163 1125 -
all-1187 -
obs--92.66 %
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)
10.45350.0570.49020.29980.1672.3855-0.0308-0.0227-0.02420.05320.04070.03110.07510.0629-0.00990.05520.02580.01380.01440.00960.0556-6.20515.085-1.417
214.10012.5302-10.17380.8083-2.0957.54630.11110.12580.29180.16890.07750.0218-0.2019-0.138-0.18870.15270.0055-0.02120.0385-0.03270.0578-7.44228.8725.103
30.1624-0.0875-0.0210.75280.36621.4123-0.0341-0.045-0.00770.08620.00070.06480.1601-0.0320.03340.06170.01650.00570.0220.01080.0357-6.82612.2141.755
43.27461.10650.96291.25310.73361.90110.07890.04620.13810.0104-0.05930.1596-0.1294-0.2268-0.01960.0510.0284-0.0040.04390.02140.0727-19.50121.567-17.018
52.0358-0.3721.88371.9579-0.48071.7670.01360.1079-0.0933-0.20030.0258-0.00590.01270.089-0.03940.09820.012-0.00680.013-0.02530.1018-2.7147.804-24.469
60.4206-0.0451-0.08970.44660.08021.1091-0.03730.04150.0995-0.01740.0175-0.0354-0.08890.08280.01980.0519-0.00170.0020.0180.01380.0583-2.23323.893-17.36
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 61
2X-RAY DIFFRACTION2A62 - 75
3X-RAY DIFFRACTION3A76 - 180
4X-RAY DIFFRACTION4A181 - 206
5X-RAY DIFFRACTION5A207 - 229
6X-RAY DIFFRACTION6A230 - 308

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