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- PDB-4jem: Crystal structure of MilB complexed with cytidine 5'-monophosphate -

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Basic information

Entry
Database: PDB / ID: 4jem
TitleCrystal structure of MilB complexed with cytidine 5'-monophosphate
ComponentsCMP/hydroxymethyl CMP hydrolase
KeywordsHYDROLASE / CMP N-glycosidase
Function / homologyNucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CYTIDINE-5'-MONOPHOSPHATE / CMP/hydroxymethyl CMP hydrolase
Function and homology information
Biological speciesStreptomyces rimofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.553 Å
AuthorsSikowitz, M.D. / Cooper, L.E. / Begley, T.P. / Kaminski, P.A. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2013
Title: Reversal of the substrate specificity of CMP N-glycosidase to dCMP.
Authors: Sikowitz, M.D. / Cooper, L.E. / Begley, T.P. / Kaminski, P.A. / Ealick, S.E.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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: CMP/hydroxymethyl CMP hydrolase
B: CMP/hydroxymethyl CMP hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4104
Polymers36,7632
Non-polymers6462
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-34 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.157, 100.386, 71.348
Angle α, β, γ (deg.)90.000, 99.630, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CMP/hydroxymethyl CMP hydrolase


Mass: 18381.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rimofaciens (bacteria) / Gene: MilB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4Y381
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M magnesium chloride, 18% PEG 8000, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2011
RadiationMonochromator: cryocooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 44996 / Num. obs: 44996 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.64 Å2 / Rsym value: 0.057 / Net I/σ(I): 25.1
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.55-1.580.3521100
1.58-1.611100
1.61-1.641100
1.64-1.67199
1.67-1.71199
1.71-1.75199

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4JEL

4jel


Resolution: 1.553→40.858 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.87 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 2270 5.05 %random
Rwork0.1862 ---
obs0.1876 44975 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.53 Å2 / Biso mean: 17.0707 Å2 / Biso min: 7.02 Å2
Refinement stepCycle: LAST / Resolution: 1.553→40.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 42 194 2591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012451
X-RAY DIFFRACTIONf_angle_d1.3223334
X-RAY DIFFRACTIONf_chiral_restr0.079369
X-RAY DIFFRACTIONf_plane_restr0.007438
X-RAY DIFFRACTIONf_dihedral_angle_d12.165868
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5529-1.58670.26381320.21032628276098
1.5867-1.62360.22571370.19126852822100
1.6236-1.66420.2021550.189226452800100
1.6642-1.70920.23191440.186526282772100
1.7092-1.75950.22911630.183426482811100
1.7595-1.81630.21361420.183326622804100
1.8163-1.88120.22971430.18526702813100
1.8812-1.95650.23831320.188226842816100
1.9565-2.04560.23721250.189227182843100
2.0456-2.15340.21371400.177826482788100
2.1534-2.28830.21371390.179126952834100
2.2883-2.4650.21141540.192726292783100
2.465-2.7130.25611380.196126882826100
2.713-3.10540.20581380.200327022840100
3.1054-3.9120.18351460.18226802826100
3.912-40.87220.21611420.17552695283799

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