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- PDB-4nt9: Crystal structure of an L,D-carboxypeptidase DacB from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 4nt9
TitleCrystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / zinc-binding
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
ACETATE ION / Peptidase M15B domain-containing protein / VanY domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.705 Å
AuthorsYang, Y.H. / Zhang, J. / Jiang, Y.L. / Zhou, C.Z. / Chen, Y.
CitationJournal: To be Published
Title: Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia
Authors: Yang, Y.H. / Zhang, J. / Jiang, Y.L. / Zhou, C.Z. / Chen, Y.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_asym_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.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.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_ref_seq_dif.details / _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
B: Putative uncharacterized protein
A: Putative uncharacterized protein
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,12713
Polymers73,3853
Non-polymers74210
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6784
Polymers24,4621
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7705
Polymers24,4621
Non-polymers3094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6784
Polymers24,4621
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.110, 68.080, 80.350
Angle α, β, γ (deg.)90.00, 108.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein / L / D-carboxypeptidase DacB


Mass: 24461.742 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 27-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0629 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q97RZ7, UniProt: A0A0H2UP74*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / 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: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-Cl, pH 8.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.705→50 Å / Num. obs: 58226 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.71→1.8 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.705→41.469 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU ML: 0.19 / σ(F): 1.35 / Phase error: 22.2 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rfree0.2119 2949 5.07 %
Rwork0.1773 --
obs0.179 58192 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.528 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å20.75 Å2
2--1.53 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.705→41.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 39 393 4833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134538
X-RAY DIFFRACTIONf_angle_d1.3756119
X-RAY DIFFRACTIONf_dihedral_angle_d14.4981649
X-RAY DIFFRACTIONf_chiral_restr0.091609
X-RAY DIFFRACTIONf_plane_restr0.007801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.705-1.7330.3097960.24481915X-RAY DIFFRACTION69
1.733-1.76280.32211230.25872177X-RAY DIFFRACTION80
1.7628-1.79490.24921360.24862657X-RAY DIFFRACTION95
1.7949-1.82940.26991450.23842650X-RAY DIFFRACTION96
1.8294-1.86680.28071430.23282652X-RAY DIFFRACTION96
1.8668-1.90740.23391290.22172694X-RAY DIFFRACTION96
1.9074-1.95170.23821390.20342665X-RAY DIFFRACTION96
1.9517-2.00050.24681410.19442660X-RAY DIFFRACTION96
2.0005-2.05460.23361480.18872670X-RAY DIFFRACTION96
2.0546-2.11510.2241500.1852674X-RAY DIFFRACTION97
2.1151-2.18330.22071280.1762690X-RAY DIFFRACTION97
2.1833-2.26140.26251360.1692682X-RAY DIFFRACTION97
2.2614-2.35190.19711560.16942706X-RAY DIFFRACTION97
2.3519-2.45890.2031270.17832709X-RAY DIFFRACTION97
2.4589-2.58860.21871550.17452717X-RAY DIFFRACTION97
2.5886-2.75070.21051370.17612728X-RAY DIFFRACTION98
2.7507-2.9630.21611760.17142682X-RAY DIFFRACTION98
2.963-3.26110.19481530.17022739X-RAY DIFFRACTION98
3.2611-3.73270.18061490.15272713X-RAY DIFFRACTION97
3.7327-4.70180.17391380.14762677X-RAY DIFFRACTION95
4.7018-41.48160.19771440.17862786X-RAY DIFFRACTION97

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