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- PDB-1oj4: Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase -

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Basic information

Entry
Database: PDB / ID: 1oj4
TitleTernary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Components4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE
KeywordsTRANSFERASE / KINASE / ISOPRENOIDS BIOSYNTHESIS / GHMP KINASE SUPERFAMILY TRANSFERASE
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL / 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.01 Å
AuthorsMiallau, L. / Alphey, M.S. / Hunter, W.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Biosynthesis of Isoprenoids: Crystal Structure of 4-Diphosphocytidyl-2C-Methyl-D-Erythritol Kinase
Authors: Miallau, L. / Alphey, M.S. / Kemp, L.E. / Leonard, G.A. / Mcsweeney, S.M. / Hecht, S. / Bacher, A. / Eisenreich, W. / Rohdich, F. / Hunter, W.N.
History
DepositionJun 30, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns_shell / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
B: 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6247
Polymers62,5332
Non-polymers2,0905
Water6,900383
1
A: 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3304
Polymers31,2671
Non-polymers1,0633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2943
Polymers31,2671
Non-polymers1,0282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.000, 76.300, 68.600
Angle α, β, γ (deg.)90.00, 107.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE / CMK / 4-(CYTIDINE-5'-DIPHOSPHO)-2-C-METHYL-D -ERYTHRITOL KINASE


Mass: 31266.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q8FI04, 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
#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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ATP + 4-(CYTIDINE 5'-DIPHOSPHO)-2-C -METHYL-D-ERYTHRITOL = ADP + 2-PHOSPHO-4- ...CATALYTIC ACTIVITY: ATP + 4-(CYTIDINE 5'-DIPHOSPHO)-2-C -METHYL-D-ERYTHRITOL = ADP + 2-PHOSPHO-4-(CYTIDINE 5'- DIPHOSPHO)-2-C-METHYL-D-ERYTHRITOL.
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % POLYETHYLENE GLYCOL 8000 0.2 M MAGNESUIM ACTETATE, 0.1M SODIUM CACODYLATE PH 6.5 20MM SULFOBETAIN
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %PEG80001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH6.5
40.25 Msulfo-betaine1reservoir
550 mMTris-HCl1droppH8.5
650 mM1dropNaCl
725 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2002 / Details: LENSES
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 39761 / % possible obs: 94.3 % / Observed criterion σ(I): 5.58 / Redundancy: 2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.89
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 5.6 / % possible all: 92.3
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 364197 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 92.3 % / Rmerge(I) obs: 0.0147 / Mean I/σ(I) obs: 5.6

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.01→65.94 Å / SU B: 3.4 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.153
Details: FURTHER REFINEMENTS SHOWED A SINGLE CONFORMATION OF THE GAMMA-PHOSHATE IN THE A-SUBUNIT
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 1972 5 %RANDOM
Rwork0.16552 ---
obs0.1674 39761 97.84 %-
Displacement parametersBiso mean: 18.254 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0.61 Å2
2---0.14 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.01→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 128 383 4868
Refinement
*PLUS
Highest resolution: 2 Å / Num. reflection Rfree: 1988 / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.01
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.33

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