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- PDB-4b4z: Crystal structure of a complex between Actinomadura R39 DD-peptid... -

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Basic information

Entry
Database: PDB / ID: 4b4z
TitleCrystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASE
KeywordsHYDROLASE / BORONIC ACID / PEPTIDOGLYCAN
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region
Similarity search - Function
D-Ala-D-Ala carboxypeptidase C, peptidase S13 / Peptidase S13, D-Ala-D-Ala carboxypeptidase C / D-Ala-D-Ala carboxypeptidase 3 (S13) family / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(bba) Sandwich / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
{[(benzylsulfonyl)amino]methyl}boronic acid / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesACTINOMADURA SP. R39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCannella, S.E. / Sauvage, E. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P.
CitationJournal: To be Published
Title: Crystal Structure of a Complex between Actinomadura R39 Dd-Peptidase and a Boronate Inhibitor
Authors: Sauvage, E.
History
DepositionAug 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 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 / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,09938
Polymers190,5884
Non-polymers3,51134
Water19,3301073
1
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,59711
Polymers47,6471
Non-polymers95010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5499
Polymers47,6471
Non-polymers9028
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5499
Polymers47,6471
Non-polymers9028
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4059
Polymers47,6471
Non-polymers7588
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.123, 90.692, 105.729
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE / DD-CARBOXYPEPTIDASE / DD-PEPTIDASE / PENICILLIN-BINDING PROTEIN / PBP


Mass: 47647.004 Da / Num. of mol.: 4 / Fragment: RESIDUES 50-515 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA SP. R39 (bacteria)
References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-BSF / {[(benzylsulfonyl)amino]methyl}boronic acid


Mass: 229.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H12BNO4S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1073 / 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: 2.39 Å3/Da / Density % sol: 48.04 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9686
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.2→35.25 Å / Num. obs: 97096 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W8Q

1w8q


Resolution: 2.2→35.25 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.732 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26035 4878 5 %RANDOM
Rwork0.20631 ---
obs0.209 92157 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13351 0 186 1073 14610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02113755
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.97518814
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96451853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69625.49572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.902151910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8821567
X-RAY DIFFRACTIONr_chiral_restr0.0750.22166
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110623
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_it0.5451.59153
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.026214515
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.52734602
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5564.54299
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 327 -
Rwork0.267 6789 -
obs--98.93 %

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