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- PDB-4jen: Structure of Clostridium botulinum CMP N-glycosidase, BcmB -

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Basic information

Entry
Database: PDB / ID: 4jen
TitleStructure of Clostridium botulinum CMP N-glycosidase, BcmB
ComponentsCMP N-GLYCOSIDASE
KeywordsHYDROLASE / CMP N-glycosidase / bacimethrin biosynthesis
Function / homologyRossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION / :
Function and homology information
Biological speciesClostridium botulinum A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 N-GLYCOSIDASE
B: CMP N-GLYCOSIDASE
C: CMP N-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5406
Polymers61,2553
Non-polymers2853
Water18010
1
A: CMP N-GLYCOSIDASE
B: CMP N-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0274
Polymers40,8372
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-43 kcal/mol
Surface area12440 Å2
MethodPISA
2
C: CMP N-GLYCOSIDASE
hetero molecules

C: CMP N-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0274
Polymers40,8372
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area2890 Å2
ΔGint-42 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.948, 104.006, 40.225
Angle α, β, γ (deg.)90.000, 97.980, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 25:45 or resseq 59:108 or resseq 114:144 )
21chain B and (resseq 25:45 or resseq 59:108 or resseq 114:144 )
31chain C and (resseq 25:45 or resseq 59:108 or resseq 114:144 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASPASPchain 'A' and (resseq 25:45 or resseq 59:108 or resseq 114:144 )AA25 - 4548 - 68
12SERSERALAALAchain 'A' and (resseq 25:45 or resseq 59:108 or resseq 114:144 )AA59 - 10882 - 131
13TYRTYRLEULEUchain 'A' and (resseq 25:45 or resseq 59:108 or resseq 114:144 )AA114 - 144137 - 167
21GLNGLNASPASPchain 'B' and (resseq 25:45 or resseq 59:108 or resseq 114:144 )BB25 - 4548 - 68
22SERSERALAALAchain 'B' and (resseq 25:45 or resseq 59:108 or resseq 114:144 )BB59 - 10882 - 131
23TYRTYRLEULEUchain 'B' and (resseq 25:45 or resseq 59:108 or resseq 114:144 )BB114 - 144137 - 167
31GLNGLNASPASPchain 'C' and (resseq 25:45 or resseq 59:108 or resseq 114:144 )CC25 - 4548 - 68
32SERSERALAALAchain 'C' and (resseq 25:45 or resseq 59:108 or resseq 114:144 )CC59 - 10882 - 131
33TYRTYRLEULEUchain 'C' and (resseq 25:45 or resseq 59:108 or resseq 114:144 )CC114 - 144137 - 167

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Components

#1: Protein CMP N-GLYCOSIDASE


Mass: 20418.285 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum A (bacteria) / Strain: ATCC 19397 / Gene: CLB_0809 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7FS24
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 18% PEG MME 2000, 0.1 M phosphate-citrate, 0.01 M spermine, 0.2 M ammonium sulfate, pH 4.4, 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: Jun 25, 2010
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: 3→50 Å / Num. all: 14604 / Num. obs: 14604 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.101 / Χ2: 1.606 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.053.50.3337381.138199.7
3.05-3.113.80.3367401.1511100
3.11-3.173.80.2727001.1051100
3.17-3.233.80.267131.2581100
3.23-3.33.80.2087511.173199.9
3.3-3.383.80.1997341.2821100
3.38-3.463.70.1757101.389199.9
3.46-3.563.70.1447241.4241100
3.56-3.663.80.137431.483199.9
3.66-3.783.70.1216971.666199.9
3.78-3.913.70.127391.7571100
3.91-4.073.70.0957461.8021100
4.07-4.263.70.0887152.237199.9
4.26-4.483.70.0767492.356199.7
4.48-4.763.70.0757042.3511100
4.76-5.133.70.0727502.395199.9
5.13-5.643.70.0767221.9991100
5.64-6.463.60.0717381.399199.7
6.46-8.133.70.0577441.304199.7
8.13-503.60.0697471.498199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JEL

4jel


Resolution: 3→34.542 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.803 / SU ML: 0.3 / σ(F): 1.35 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 737 5.05 %random
Rwork0.2343 ---
obs0.2352 14580 99.17 %-
all-14580 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.94 Å2 / Biso mean: 65.1795 Å2 / Biso min: 32.94 Å2
Refinement stepCycle: LAST / Resolution: 3→34.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 15 10 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032757
X-RAY DIFFRACTIONf_angle_d0.5423738
X-RAY DIFFRACTIONf_chiral_restr0.037435
X-RAY DIFFRACTIONf_plane_restr0.002459
X-RAY DIFFRACTIONf_dihedral_angle_d8.928944
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A782X-RAY DIFFRACTIONPOSITIONAL0.011
12B782X-RAY DIFFRACTIONPOSITIONAL0.011
13C748X-RAY DIFFRACTIONPOSITIONAL0.008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9939-3.22490.2961480.26132678282697
3.2249-3.54920.28811530.238827802933100
3.5492-4.06210.26121580.228327642922100
4.0621-5.11510.21981480.20827922940100
5.1151-34.54450.23481300.25142829295999

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