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- PDB-4uz3: Crystal structure of the N-terminal LysM domains from the putativ... -

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Basic information

Entry
Database: PDB / ID: 4uz3
TitleCrystal structure of the N-terminal LysM domains from the putative NlpC/P60 D,L endopeptidase from T. thermophilus bound to N-acetyl-chitohexaose
ComponentsCELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN
KeywordsHYDROLASE
Function / homology
Function and homology information


Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Papain-like cysteine peptidase superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Cell wall-binding endopeptidase-related protein
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWong, J.E.M.M. / Blaise, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: An Intermolecular Binding Mechanism Involving Multiple Lysm Domains Mediates Carbohydrate Recognition by an Endopeptidase.
Authors: Wong, J.E.M.M. / Midtgaard, S.R. / Gysel, K. / Thygesen, M.B. / Sorensen, K.K. / Jensen, K.J. / Stougaard, J. / Thirup, S. / Blaise, M.
History
DepositionSep 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN
B: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN
C: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,31212
Polymers32,9153
Non-polymers4,3979
Water7,080393
1
A: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9477
Polymers10,9721
Non-polymers2,9766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0682
Polymers10,9721
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2973
Polymers10,9721
Non-polymers1,3252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.490, 105.490, 105.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2196-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN / P60_TTH


Mass: 10971.500 Da / Num. of mol.: 3 / Fragment: LYSM DOMAIN, RESIDUES 16-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q5SLM7

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Sugars , 4 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 398 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.97 Å3/Da / Density % sol: 58.61 % / Description: NONE
Crystal growDetails: 0.1 M MES PH6.5, 1.6 M AMMONIUM SULFATE, 5% DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 39631 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Biso Wilson estimate: 14.78 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 20.3
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→19.589 Å / SU ML: 0.16 / σ(F): 1.37 / Phase error: 17.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 1987 5 %
Rwork0.1519 --
obs0.1538 39631 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.7 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 327 393 2578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052354
X-RAY DIFFRACTIONf_angle_d0.9153241
X-RAY DIFFRACTIONf_dihedral_angle_d10.752889
X-RAY DIFFRACTIONf_chiral_restr0.043426
X-RAY DIFFRACTIONf_plane_restr0.004385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7502-1.79390.24431350.19372686X-RAY DIFFRACTION100
1.7939-1.84240.26421410.18642657X-RAY DIFFRACTION100
1.8424-1.89650.22841410.18322639X-RAY DIFFRACTION100
1.8965-1.95770.20981420.16062682X-RAY DIFFRACTION100
1.9577-2.02760.19641400.15312648X-RAY DIFFRACTION100
2.0276-2.10870.19331400.15172675X-RAY DIFFRACTION100
2.1087-2.20450.18721430.14512683X-RAY DIFFRACTION100
2.2045-2.32060.17211450.14962648X-RAY DIFFRACTION100
2.3206-2.46570.19261400.15592680X-RAY DIFFRACTION100
2.4657-2.65570.23261430.15582698X-RAY DIFFRACTION100
2.6557-2.92220.19941450.162695X-RAY DIFFRACTION100
2.9222-3.34320.1741370.14752704X-RAY DIFFRACTION100
3.3432-4.20520.15781440.12652723X-RAY DIFFRACTION100
4.2052-19.59020.16951510.15162826X-RAY DIFFRACTION100

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