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- PDB-4d0y: Crystal structure of DacB from Streptococcus pneumoniae D39 -

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Basic information

Entry
Database: PDB / ID: 4d0y
TitleCrystal structure of DacB from Streptococcus pneumoniae D39
ComponentsDACB
KeywordsHYDROLASE / L-D-CARBOXIPEPTIDASE / PNEUMOCOCCUS
Function / homology
Function and homology information


peptidase activity / proteolysis / metal ion binding
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Lipoprotein, putative / Lipoprotein, putative
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGutierrez-Fernandez, J. / Hermoso, J.A.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structure of the Pneumococcal L,D-Carboxypeptidase Dacb and Pathophysiological Effects of Disabled Cell Wall Hydrolases Daca and Dacb.
Authors: Abdullah, M.R. / Gutierrez-Fernandez, J. / Pribyl, T. / Gisch, N. / Saleh, M. / Rohde, M. / Petruschka, L. / Burchhardt, G. / Schwudke, D. / Hermoso, J.A. / Hammerschmidt, S.
History
DepositionApr 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2May 8, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: DACB
B: DACB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,74817
Polymers41,7082
Non-polymers1,04015
Water8,629479
1
A: DACB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2767
Polymers20,8541
Non-polymers4226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DACB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,47210
Polymers20,8541
Non-polymers6189
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.950, 37.634, 102.837
Angle α, β, γ (deg.)90.00, 97.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 55 - 238 / Label seq-ID: 1 - 184

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.996, 0.087, 0.017), (0.088, 0.996, 0.017), (-0.016, 0.019, -1)
Vector: 17.32, 17.657, 50.782)

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Components

#1: Protein DACB / LIPOPROTEIN / PUTATIVE


Mass: 20853.848 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 55-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE D39 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q04LP8, UniProt: A0A0H2ZP28*PLUS, muramoyltetrapeptide carboxypeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growpH: 8
Details: 0.01 M ZINC CHLORIDE, 0.1 M TRIS-HCL PH 8.0, 14% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50.92 Å / Num. obs: 26483 / % possible obs: 99.7 % / Observed criterion σ(I): 2.3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→101.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.253 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24263 1276 4.8 %RANDOM
Rwork0.18114 ---
obs0.18409 25196 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.168 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å20.55 Å2
2---0.9 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2→101.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 23 479 3452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193070
X-RAY DIFFRACTIONr_bond_other_d0.0050.022697
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.9554096
X-RAY DIFFRACTIONr_angle_other_deg1.14636241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66925.062162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69215498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1131510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023504
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02702
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_it1.8182.1681470
X-RAY DIFFRACTIONr_mcbond_other1.8152.1661469
X-RAY DIFFRACTIONr_mcangle_it2.823.2431834
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1582.4961600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 9858 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 98 -
Rwork0.252 1834 -
obs--98.82 %

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