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- PDB-4ed4: Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythr... -

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Basic information

Entry
Database: PDB / ID: 4ed4
TitleCrystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abcessus, bound to 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 / 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
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 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)33,2502
Polymers32,7431
Non-polymers5071
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.450, 53.360, 109.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-556-

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-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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Internal tracking number 231560F1, CSHT screen condition F1: 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate, pH 4.6, 30% PEG2000 MME, MyabA.00725.a.A1 PW30213 at 29.3 mg/mL in 25 mM ...Details: Internal tracking number 231560F1, CSHT screen condition F1: 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate, pH 4.6, 30% PEG2000 MME, 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 ATP, 2 mM EBSI1799, 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: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→42.738 Å / Num. obs: 26899 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 20.012 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 31.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.85.850.14310.810158173684.2
1.8-1.840.12612.411255174587.2
1.84-1.90.10514.411322171890
1.9-1.960.09316.611472174192.1
1.96-2.020.07919.111745174994.6
2.02-2.090.07221.911596169696.6
2.09-2.170.06725.312683167698.4
2.17-2.260.06329.514054163498.9
2.26-2.360.0632.114500158499.1
2.36-2.470.05834.814324149999.1
2.47-2.610.05835.814706144499.2
2.61-2.770.05439.815230137699.4
2.77-2.960.0474716835128999.5
2.96-3.20.04550.215938120099.4
3.2-3.50.04254.814535110799.2
3.5-3.910.03957.513362102798.8
3.91-4.520.03859.71174090199.2
4.52-5.530.03658.21002378099.9
5.53-7.830.03555.18077625100
7.83-42.7380.03157.5440437299.7

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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→42.738 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.522 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1370 5.1 %RANDOM
Rwork0.166 ---
obs0.169 26898 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.343 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 31 245 2410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192241
X-RAY DIFFRACTIONr_bond_other_d0.0010.021400
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9693081
X-RAY DIFFRACTIONr_angle_other_deg0.86433429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1335309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92624.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95815305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.521515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02446
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 83 -
Rwork0.165 1516 -
all-1599 -
obs--82.89 %
Refinement TLS params.Method: refined / Origin x: -16.851 Å / Origin y: 7.13 Å / Origin z: -16.821 Å
111213212223313233
T0.0314 Å20.0056 Å20.0116 Å2-0.0268 Å20.0129 Å2--0.0094 Å2
L0.2588 °2-0.1651 °2-0.1827 °2-1.2745 °20.1912 °2--0.4119 °2
S-0.0557 Å °0.0003 Å °-0.0221 Å °0.0565 Å °0.0202 Å °0.0446 Å °0.0679 Å °0.0385 Å °0.0355 Å °

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