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- PDB-4anr: Crystal structure of soluble lytic Transglycosylase SltB1 from Ps... -

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Basic information

Entry
Database: PDB / ID: 4anr
TitleCrystal structure of soluble lytic Transglycosylase SltB1 from Pseudomonas aeruginosa
ComponentsSOLUBLE LYTIC TRANSGLYCOSYLASE B
KeywordsLYASE / EF-HAND LIKE MOTIF / PEPTIDOGLYCAN
Function / homology
Function and homology information


peptidoglycan lytic transglycosylase activity / peptidoglycan catabolic process / metal ion binding
Similarity search - Function
Bacterial muramidase / Lytic transglycosylase MltB / Transglycosylase SLT domain 2 / Membrane-bound lytic murein transglycosylase B-like / Transglycosylase SLT domain / Helicase, Ruva Protein; domain 3 / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Soluble lytic transglycosylase B
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsNikolaidis, I. / Izore, T. / Job, V. / Thielens, N. / Breukink, E. / Dessen, A.
CitationJournal: Microb.Drug Resist. / Year: 2012
Title: Calcium-Dependent Complex Formation between Pbp2 and Lytic Transglycosylase Sltb1 of Pseudomonas Aeruginosa.
Authors: Nikolaidis, I. / Izore, T. / Job, V. / Thielens, N. / Breukink, E. / Dessen, A.
History
DepositionMar 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_conn.ptnr2_label_seq_id / _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: SOLUBLE LYTIC TRANSGLYCOSYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4042
Polymers36,3641
Non-polymers401
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.500, 91.500, 81.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SOLUBLE LYTIC TRANSGLYCOSYLASE B / LYTIC TRANSGLYCOSYLASE SLTB1


Mass: 36363.773 Da / Num. of mol.: 1 / Fragment: CALCIUM-BINDING DOMAIN, RESIDUES 38-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PETDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9HX24
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCALCIUM ION (CA): THE COORDINATION OF THE CALCIUM ION REPRESENTS THE TYPICAL BIPYRAMIDAL ...CALCIUM ION (CA): THE COORDINATION OF THE CALCIUM ION REPRESENTS THE TYPICAL BIPYRAMIDAL CONFIGURATION FOR EF-HAND-LIKE MOTIFS.
Sequence detailsN-TERMINAL HIS-TAG AND THROMBIN SITE

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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: 2.81 Å3/Da / Density % sol: 56.22 % / Description: NONE
Crystal growpH: 6.5
Details: 1.5 M MALONATE PH 6.5 AND 3 MM CACL2, 20MG/ML PROTEIN CONCENTRATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.84→45.75 Å / Num. obs: 34561 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 21 % / Biso Wilson estimate: 28.263 Å2 / Rsym value: 0.06 / Net I/σ(I): 41.29
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 20 % / Mean I/σ(I) obs: 8.41 / Rsym value: 0.46 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QUS

1qus


Resolution: 1.84→45.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.286 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21121 3439 10 %RANDOM
Rwork0.1783 ---
obs0.18163 31078 100 %-
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: 24.106 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.84→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 1 186 2547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222425
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9413283
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90922.541122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52615392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7851526
X-RAY DIFFRACTIONr_chiral_restr0.1110.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211895
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.871.51477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.97322367
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6113948
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.3424.5914
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 268 -
Rwork0.201 2272 -
obs--100 %

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