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- PDB-6azi: 1.75 Angstrom Resolution Crystal Structure of D-alanyl-D-alanine ... -

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Basic information

Entry
Database: PDB / ID: 6azi
Title1.75 Angstrom Resolution Crystal Structure of D-alanyl-D-alanine Endopeptidase from Enterobacter cloacae in Complex with Covalently Bound Boronic Acid
ComponentsD-alanyl-D-alanine endopeptidase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / D-alanyl-D-alanine Endopeptidase / Boronic Acid.
Function / homologyPeptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / Beta-lactamase/transpeptidase-like / proteolysis / BORATE ION / D-alanyl-D-alanine endopeptidase
Function and homology information
Biological speciesEnterobacter cloacae subsp. cloacae ATCC 13047 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionSep 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 2.0May 31, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_validate_close_contact / struct_asym / struct_conn
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _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.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Revision 2.2Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-alanyl-D-alanine endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9372
Polymers31,8581
Non-polymers791
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-0 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.470, 64.233, 79.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-alanyl-D-alanine endopeptidase


Mass: 31857.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae ATCC 13047 (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_03445 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) magic / References: UniProt: A0A0H3CN11
#2: Chemical ChemComp-BO4 / BORATE ION


Mass: 78.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 9.0 mg/mL protein in 0.01 M Tris-HCl, pH 8.3 against screen PACT (B5), 0.1 M MIB buffer, pH 8.0, 25% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 19, 2017 / Details: C(111)
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 25532 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.058 / Rsym value: 0.118 / Χ2: 2.308 / Net I/σ(I): 17.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2 / Num. unique obs: 1312 / CC1/2: 0.767 / Rpim(I) all: 0.334 / Rsym value: 0.664 / Χ2: 0.996 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→29.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.646 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23806 1240 4.9 %RANDOM
Rwork0.18787 ---
obs0.1903 24120 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.17 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2---1.05 Å20 Å2
3----2.21 Å2
Refinement stepCycle: 1 / Resolution: 1.75→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 0 265 2227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192093
X-RAY DIFFRACTIONr_bond_other_d0.0020.021993
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9782848
X-RAY DIFFRACTIONr_angle_other_deg0.82234619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2885269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96823.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85415330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2431516
X-RAY DIFFRACTIONr_chiral_restr0.0540.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.0212334
X-RAY DIFFRACTIONr_gen_planes_other0.020.02422
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_it1.5472.0341052
X-RAY DIFFRACTIONr_mcbond_other1.5362.0281051
X-RAY DIFFRACTIONr_mcangle_it2.2593.0291329
X-RAY DIFFRACTIONr_mcangle_other2.2593.0371330
X-RAY DIFFRACTIONr_scbond_it2.212.351041
X-RAY DIFFRACTIONr_scbond_other2.2092.3561042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5093.4331520
X-RAY DIFFRACTIONr_long_range_B_refined5.41825.5252443
X-RAY DIFFRACTIONr_long_range_B_other5.22725.1722389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 92 -
Rwork0.323 1805 -
obs--99.79 %

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