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

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Basic information

Entry
Database: PDB / ID: 4emd
TitleCrystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abcessus, bound to CMP and SO4
Components4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
KeywordsTRANSFERASE / SSGCID / NIH / NIAID / SBRI / 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 / 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
CYTIDINE-5'-MONOPHOSPHATE / 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionApr 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 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)33,1623
Polymers32,7431
Non-polymers4192
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.440, 109.930, 53.100
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-549-

HOH

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Components

#1: Protein 4-diphosphocytidyl-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


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Internal tracking number 230821D4, JCSG screen condition D4: 30% PEG8000, acetate, pH 4.5, 200 mM lithium sulfate, MyabA.00725.a.A1 PW30213 at 29.3 mg/mL in 25 mM HEPES, pH 7.0, 500 mM ...Details: Internal tracking number 230821D4, JCSG screen condition D4: 30% PEG8000, acetate, pH 4.5, 200 mM lithium sulfate, 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: 20% ethylene glycol, 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: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 28202 / Num. obs: 28123 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.25 % / Biso Wilson estimate: 19.352 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 30.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.82.540.4542.35090200597.4
1.8-1.840.4222.75617200199.7
1.84-1.90.31157270193499.5
1.9-1.960.2447.98968187899.8
1.96-2.020.18511.610627184899.9
2.02-2.090.14316.412015174399.9
2.09-2.170.12921.4154881721100
2.17-2.260.1128189021656100
2.26-2.360.09730.8189451604100
2.36-2.470.09232.4183651517100
2.47-2.610.08534.3182441465100
2.61-2.770.07837.4178281373100
2.77-2.960.06543.9184611312100
2.96-3.20.05251.9172551205100
3.2-3.50.04362161951136100
3.5-3.910.03676.2144151025100
3.91-4.520.0386.412753916100
4.52-5.530.03276.810825783100
5.53-7.830.03864.48496627100
7.830.02588446837499.2

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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 4DXL

4dxl


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.024 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1424 5.1 %RANDOM
Rwork0.159 ---
obs0.161 28123 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.579 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 26 292 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192232
X-RAY DIFFRACTIONr_bond_other_d0.0020.021410
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9653060
X-RAY DIFFRACTIONr_angle_other_deg0.89833443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.685308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13423.87193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42715307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4841517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 93 -
Rwork0.244 1745 -
all-1838 -
obs--97.04 %
Refinement TLS params.Method: refined / Origin x: 6.7522 Å / Origin y: -16.6394 Å / Origin z: -7.3443 Å
111213212223313233
T0.0104 Å20.0075 Å2-0.0017 Å2-0.0135 Å2-0.0113 Å2--0.0254 Å2
L0.1168 °2-0.025 °20.0722 °2-0.2299 °2-0.2005 °2--0.7829 °2
S-0.0255 Å °-0.0075 Å °-0.0235 Å °0.0343 Å °0.0181 Å °-0.0213 Å °-0.0454 Å °-0.0248 Å °0.0074 Å °

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