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- PDB-4jel: Structure of MilB Streptomyces rimofaciens CMP N-glycosidase -

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Basic information

Entry
Database: PDB / ID: 4jel
TitleStructure of MilB Streptomyces rimofaciens CMP N-glycosidase
ComponentsCMP/hydroxymethyl CMP hydrolase
KeywordsHYDROLASE / CMP N-glycosidase / mildiomycin biosynthesis
Function / homologyNucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CMP/hydroxymethyl CMP hydrolase
Function and homology information
Biological speciesStreptomyces rimofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.952 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 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: CMP/hydroxymethyl CMP hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7413
Polymers20,5491
Non-polymers1922
Water1,946108
1
A: CMP/hydroxymethyl CMP hydrolase
hetero molecules

A: CMP/hydroxymethyl CMP hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4836
Polymers41,0982
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area3020 Å2
ΔGint-80 kcal/mol
Surface area13140 Å2
MethodPISA
2
A: CMP/hydroxymethyl CMP hydrolase
hetero molecules

A: CMP/hydroxymethyl CMP hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4836
Polymers41,0982
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+5/31
Buried area1980 Å2
ΔGint-61 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.819, 97.819, 61.893
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-340-

HOH

31A-406-

HOH

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Components

#1: Protein CMP/hydroxymethyl CMP hydrolase


Mass: 20549.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rimofaciens (bacteria) / Gene: MilB / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: B4Y381
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 8% PEG 1000, 0.1 M phosphate-citrate, 0.2 M lithium sulfate, pH 4.2, 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: Oct 20, 2010
RadiationMonochromator: Cryo-cooled 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: 1.95→50 Å / Num. all: 24181 / Num. obs: 23697 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 27.96 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 40.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.95-1.98196.9
1.98-2.02197.8
2.02-2.06196.7
2.06-2.1197.9
2.1-2.15197.7
2.15-2.2197.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.952→42.357 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8582 / SU ML: 0.18 / σ(F): 1.89 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1168 4.93 %random
Rwork0.1981 ---
obs0.2002 23688 98.27 %-
all-23697 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.42 Å2 / Biso mean: 26.5855 Å2 / Biso min: 12.43 Å2
Refinement stepCycle: LAST / Resolution: 1.952→42.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1149 0 10 108 1267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071183
X-RAY DIFFRACTIONf_angle_d1.0831607
X-RAY DIFFRACTIONf_chiral_restr0.071176
X-RAY DIFFRACTIONf_plane_restr0.005212
X-RAY DIFFRACTIONf_dihedral_angle_d11.833417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9524-2.04120.24211670.19872780294797
2.0412-2.14880.22831630.18912753291698
2.1488-2.28350.24311550.19262802295798
2.2835-2.45970.24711220.19352836295898
2.4597-2.70720.2491460.20032804295098
2.7072-3.09890.23861560.20412824298099
3.0989-3.90380.23731310.19592843297499
3.9038-42.36680.25251280.20052878300699

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