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- PDB-3itb: Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. ... -

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Basic information

Entry
Database: PDB / ID: 3itb
TitleCrystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in complex with a substrate fragment
Components
  • D-alanyl-D-alanine carboxypeptidase DacC
  • Peptidoglycan substrate (AMV)A(FGA)K(DAL)(DAL)
KeywordsHYDROLASE / Penicillin-Binding Protein / PBP6 / DD-carboxypeptidase / peptidoglycan / substrate fragment / Carboxypeptidase / Cell inner membrane / Cell membrane / Cell shape / Cell wall biogenesis/degradation / Membrane / Peptidoglycan synthesis / Protease
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space / response to xenobiotic stimulus / protein homodimerization activity ...serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space / response to xenobiotic stimulus / protein homodimerization activity / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase ...Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
sucrose / Chem-AMV / D-alanyl-D-alanine carboxypeptidase DacC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, Y. / Zhang, W. / Shi, Q. / Hesek, D. / Lee, M. / Mobashery, S. / Shoichet, B.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Crystal structures of penicillin-binding protein 6 from Escherichia coli.
Authors: Chen, Y. / Zhang, W. / Shi, Q. / Hesek, D. / Lee, M. / Mobashery, S. / Shoichet, B.K.
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Mar 27, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _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.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 3.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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 DacC
B: D-alanyl-D-alanine carboxypeptidase DacC
C: D-alanyl-D-alanine carboxypeptidase DacC
D: D-alanyl-D-alanine carboxypeptidase DacC
L: Peptidoglycan substrate (AMV)A(FGA)K(DAL)(DAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,08113
Polymers152,8555
Non-polymers1,2268
Water12,592699
1
A: D-alanyl-D-alanine carboxypeptidase DacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1872
Polymers38,0911
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanyl-D-alanine carboxypeptidase DacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3794
Polymers38,0911
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-alanyl-D-alanine carboxypeptidase DacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5303
Polymers38,0911
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-alanyl-D-alanine carboxypeptidase DacC
L: Peptidoglycan substrate (AMV)A(FGA)K(DAL)(DAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9844
Polymers38,5812
Non-polymers4032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.534, 185.351, 82.329
Angle α, β, γ (deg.)90.00, 100.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12D
22A
13D
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUGLUGLU3CC290290
211GLUGLUGLUGLU3DD290290
121GLYGLYASPASP4CC90 - 9190 - 91
221GLYGLYASPASP4DD90 - 9190 - 91
112GLYGLYASPASP3DD90 - 9190 - 91
212GLYGLYASPASP3AA90 - 9190 - 91
113GLYGLYASPASP3DD90 - 9190 - 91
213GLYGLYASPASP3BB90 - 9190 - 91

NCS ensembles :
ID
1
2
3

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ABCDL

#1: Protein
D-alanyl-D-alanine carboxypeptidase DacC / DD-carboxypeptidase / DD-peptidase / Penicillin-binding protein 6 / PBP-6


Mass: 38091.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dacC, b0839, JW0823 / Plasmid: PET-24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08506, serine-type D-Ala-D-Ala carboxypeptidase
#2: Protein/peptide Peptidoglycan substrate (AMV)A(FGA)K(DAL)(DAL)


Mass: 489.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 2 molecules

#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-AMV / methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside / METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE / methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucoside / methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-D-glucoside / methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-glucoside / Methyl group


Type: D-saccharide / Mass: 307.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H21NO8

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Non-polymers , 2 types, 705 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 8000, pH 4.5, vapor diffusion, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Apr 10, 2009 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 136723 / % possible obs: 88 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.07 / Χ2: 1.107 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.862.20.59129971.293184
1.86-1.942.20.422132361.188185.4
1.94-2.032.30.266132571.05185.3
2.03-2.132.30.188130731.03184.3
2.13-2.272.30.154130341.063184
2.27-2.442.30.133131961.083185
2.44-2.692.20.113137021.034188.3
2.69-3.082.20.094146221.071193.9
3.08-3.882.20.067150371.132196.4
3.88-502.30.046145691.141192.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0072phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo PBP6 model

Resolution: 1.8→40.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.301 / WRfactor Rwork: 0.242 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.797 / SU B: 3.31 / SU ML: 0.101 / SU R Cruickshank DPI: 0.145 / SU Rfree: 0.144 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.254 6831 5 %RANDOM
Rwork0.205 ---
obs0.207 136655 87.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.58 Å2 / Biso mean: 38.923 Å2 / Biso min: 19.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å20.27 Å2
2---2.87 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10613 0 53 699 11365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210954
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.97614852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.31851402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95925.045448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.198151895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5841554
X-RAY DIFFRACTIONr_chiral_restr0.1780.21710
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218126
X-RAY DIFFRACTIONr_mcbond_it2.291.56913
X-RAY DIFFRACTIONr_mcangle_it3.512211106
X-RAY DIFFRACTIONr_scbond_it5.26134041
X-RAY DIFFRACTIONr_scangle_it8.0514.53744
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C4TIGHT POSITIONAL0.080.05
1C12MEDIUM POSITIONAL0.170.5
1C5LOOSE POSITIONAL0.715
1C4TIGHT THERMAL2.340.5
1C12MEDIUM THERMAL1.372
1C5LOOSE THERMAL1.5710
2D8TIGHT POSITIONAL0.050.05
2D4LOOSE POSITIONAL0.135
2D8TIGHT THERMAL1.430.5
2D4LOOSE THERMAL2.4910
3D8TIGHT POSITIONAL0.050.05
3D4LOOSE POSITIONAL0.125
3D8TIGHT THERMAL2.350.5
3D4LOOSE THERMAL3.5910
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 467 -
Rwork0.373 8944 -
all-9411 -
obs--82.13 %

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