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- PDB-3qay: Catalytic domain of CD27L endolysin targeting Clostridia Difficile -

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Basic information

Entry
Database: PDB / ID: 3qay
TitleCatalytic domain of CD27L endolysin targeting Clostridia Difficile
ComponentsEndolysin
KeywordsLYASE / Amidase a/b fold
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / metal ion binding
Similarity search - Function
Zn-dependent exopeptidases / : / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesClostridium phage phiCD27 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMayer, M.J. / Garefaliki, V. / Spoerl, R. / Narbad, A. / Meijers, R.
CitationJournal: J.Bacteriol. / Year: 2011
Title: Structure-based modification of a Clostridium difficile-targeting endolysin affects activity and host range.
Authors: Mayer, M.J. / Garefalaki, V. / Spoerl, R. / Narbad, A. / Meijers, R.
History
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Endolysin
B: Endolysin
C: Endolysin
D: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,84022
Polymers80,2484
Non-polymers1,59118
Water20,5731142
1
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4125
Polymers20,0621
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5076
Polymers20,0621
Non-polymers4455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4125
Polymers20,0621
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5076
Polymers20,0621
Non-polymers4455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.507, 69.737, 78.818
Angle α, β, γ (deg.)101.72, 102.00, 105.24
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Endolysin


Mass: 20062.072 Da / Num. of mol.: 4 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phage phiCD27 (virus) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: B6SBV8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1142 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1 M Tris-HCl, 0.2 M LiSO4, 20 % PEG 4000, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 6, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.87→20 Å / Num. all: 58273 / Num. obs: 50589 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.9
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 / % possible all: 69.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XOV

1xov


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.864 / SU B: 10.646 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24571 2166 5 %RANDOM
Rwork0.18383 ---
obs0.18698 41298 91.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.946 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.81 Å2-0.38 Å2
2---0.99 Å2-0.11 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5620 0 74 1142 6836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225764
X-RAY DIFFRACTIONr_bond_other_d0.0010.023964
X-RAY DIFFRACTIONr_angle_refined_deg0.9831.9887748
X-RAY DIFFRACTIONr_angle_other_deg0.74939756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82125.167240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87151104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9181520
X-RAY DIFFRACTIONr_chiral_restr0.0550.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021064
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3171.53556
X-RAY DIFFRACTIONr_mcbond_other0.0631.51480
X-RAY DIFFRACTIONr_mcangle_it0.60225708
X-RAY DIFFRACTIONr_scbond_it0.98832208
X-RAY DIFFRACTIONr_scangle_it1.624.52040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 147 -
Rwork0.197 2875 -
obs--85.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7735-0.2894-0.07651.1458-0.10421.4037-0.0155-0.02520.0143-0.0115-0.01630.01550.02050.01670.03180.00670.00530.00630.0342-0.0070.01280.142-0.378-0.299
20.70050.1742-0.05240.87390.12561.25040.0016-0.03560.02070.008-0.04550.00930.0461-0.01550.04380.00320.00450.00280.0322-0.00610.011-20.599-20.31236.408
30.69330.28690.00721.4289-0.13221.28230.00770.0246-0.02410.04280.0007-0.0245-0.0233-0.0021-0.00850.00420.0083-0.00490.0286-0.01050.02061.264-53.46136.945
40.6932-0.3785-0.01091.69870.17440.83470.01720.0180.0258-0.0457-0.0234-0.04260.0074-0.00580.00620.02870.01080.00050.0254-0.00470.018414.457-33.5010.468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 179
2X-RAY DIFFRACTION2B0 - 179
3X-RAY DIFFRACTION3C0 - 179
4X-RAY DIFFRACTION4D0 - 179

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