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- PDB-5zhw: VanYB in complex with D-Alanine-D-Alanine -

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Basic information

Entry
Database: PDB / ID: 5zhw
TitleVanYB in complex with D-Alanine-D-Alanine
ComponentsD-alanyl-D-alanine carboxypeptidase
KeywordsHYDROLASE / Vancomycin resistance / peptidase / metallopeptidase family M15
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M15B / : / D-alanyl-D-alanine carboxypeptidase / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / D-ALANINE / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesEnterococcus faecalis V583 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsKim, H.S. / Hahn, H.
Funding support Korea, Republic Of, 6items
OrganizationGrant numberCountry
Korea Ministry of Science, ICT and Future Planning2013R1A2A1A05067303 Korea, Republic Of
Korea Ministry of Science and ICTNRF-2011-0030001 Korea, Republic Of
Korea Ministry of Science and ICTNRF-2013M3A6A4043695 Korea, Republic Of
Korea Ministry of Science and ICTNRF-2017R1C1B2012225 Korea, Republic Of
National Cancer Center Grant of KoreaNCC-1120170 Korea, Republic Of
Korea Ministry of EducationNRF-2017R1A6A3A01002416 Korea, Republic Of
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB.
Authors: Kim, H.S. / Hahn, H. / Kim, J. / Jang, D.M. / Lee, J.Y. / Back, J.M. / Im, H.N. / Kim, H. / Han, B.W. / Suh, S.W.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,71412
Polymers51,6582
Non-polymers1,05610
Water1,946108
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A: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3576
Polymers25,8291
Non-polymers5285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3576
Polymers25,8291
Non-polymers5285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.861, 40.578, 115.449
Angle α, β, γ (deg.)90.00, 108.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-alanyl-D-alanine carboxypeptidase / DD-peptidase


Mass: 25829.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis V583 (bacteria) / Strain: ATCC 700802 / V583 / Gene: vanYB, EF_2297 / Production host: Escherichia coli (E. coli)
References: UniProt: Q47746, serine-type D-Ala-D-Ala carboxypeptidase

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Non-polymers , 5 types, 118 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: PEG 1500, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 19873 / % possible obs: 98.8 % / Redundancy: 2.6 % / Net I/σ(I): 17.6
Reflection shellResolution: 2.18→2.22 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZHF

5zhf


Resolution: 2.18→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.941 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20755 988 5 %RANDOM
Rwork0.15906 ---
obs0.16142 18878 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å20.31 Å2
2--0 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.18→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 56 108 3088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193042
X-RAY DIFFRACTIONr_bond_other_d0.0020.022714
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9564124
X-RAY DIFFRACTIONr_angle_other_deg0.9463.0066302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7125360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02424.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71915482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5041520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213400
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02624
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_it2.2733.5481452
X-RAY DIFFRACTIONr_mcbond_other2.273.5481452
X-RAY DIFFRACTIONr_mcangle_it3.5465.2931808
X-RAY DIFFRACTIONr_mcangle_other3.5465.2961809
X-RAY DIFFRACTIONr_scbond_it3.1534.0321589
X-RAY DIFFRACTIONr_scbond_other3.1524.0341590
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9535.8822316
X-RAY DIFFRACTIONr_long_range_B_refined6.53641.5453463
X-RAY DIFFRACTIONr_long_range_B_other6.53541.5633464
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.177→2.233 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 72 -
Rwork0.201 1357 -
obs--97.28 %

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