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- PDB-5fsr: Crystal structure of penicillin binding protein 6B from Escherich... -

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Basic information

Entry
Database: PDB / ID: 5fsr
TitleCrystal structure of penicillin binding protein 6B from Escherichia coli
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASE DACD
KeywordsHYDROLASE / DD-CARBOXYPEPTIDASE / DACD / PENICILLIN BINDING PROTEIN / PEPTIDOGLYCAN
Function / homology
Function and homology information


peptidoglycan metabolic process / 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 / beta-lactamase activity / regulation of cell shape / plasma membrane
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-alanyl-D-alanine carboxypeptidase DacD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPeters, K. / Kannan, S. / Rao, V.A. / Bilboy, J. / Vollmer, D. / Erickson, S.W. / Lewis, R.J. / Young, K.D. / Vollmer, W.
CitationJournal: Mbio / Year: 2016
Title: The Redundancy of Peptidoglycan Carboxypeptidases Ensures Robust Cell Shape Maintenance in Escherichia Coli
Authors: Peters, K. / Kannan, S. / Rao, V.A. / Bilboy, J. / Vollmer, D. / Erickson, S.W. / Lewis, R.J. / Young, K.D. / Vollmer, W.
History
DepositionJan 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
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 / _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

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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 DACD
B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE DACD


Theoretical massNumber of molelcules
Total (without water)83,8182
Polymers83,8182
Non-polymers00
Water3,099172
1
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE DACD


Theoretical massNumber of molelcules
Total (without water)41,9091
Polymers41,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE DACD


Theoretical massNumber of molelcules
Total (without water)41,9091
Polymers41,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.252, 55.996, 108.137
Angle α, β, γ (deg.)104.88, 95.24, 90.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: -14 - 346 / Label seq-ID: 9 - 368

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

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Components

#1: Protein D-ALANYL-D-ALANINE CARBOXYPEPTIDASE DACD / DD-CARBOXYPEPTIDASE / DD-PEPTIDASE / PENICILLIN-BINDING PROTEIN 6B / PBP-6B


Mass: 41908.969 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 22-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P33013, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SIGNAL PEPTIDE SEQUENCE HAS BEEN REMOVED (21 RESIDUES)AND THE C-TERMINAL AMPHIPATHIC ...N-TERMINAL SIGNAL PEPTIDE SEQUENCE HAS BEEN REMOVED (21 RESIDUES)AND THE C-TERMINAL AMPHIPATHIC HELIX HAS BEEN REMOVED (14 RESIDUES).

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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: 2.45 Å3/Da / Density % sol: 49.89 % / Description: NONE
Crystal growpH: 5.5 / Details: 20 % PEG 3000, 0.1 M SODIUM CITRATE, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97901
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.4→43.59 Å / Num. obs: 29631 / % possible obs: 95.2 % / Observed criterion σ(I): 1.5 / Redundancy: 1.9 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.3 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NZO

1nzo


Resolution: 2.4→43.59 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.816 / SU B: 26.038 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED RESIDUES 273-289, 310-322 AND 347--353 ARE DISORDERED AND THEREFORE NOT MODELLED. THE FOLLOWING RESIDUES HAVE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED RESIDUES 273-289, 310-322 AND 347--353 ARE DISORDERED AND THEREFORE NOT MODELLED. THE FOLLOWING RESIDUES HAVE DISORDERED SIDE-CHAIN ATOMS THAT HAVE NOT BEEN MODELLED CHAIN A - 90,203,272,324,325,326,327 CHAIN B - 2,77,201,203,312,327 DISORDERED ATOMS WERE REMOVED
RfactorNum. reflection% reflectionSelection details
Rfree0.30249 1542 5.2 %RANDOM
Rwork0.25735 ---
obs0.25979 28083 95.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.521 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å20.72 Å2-0.39 Å2
2--0.39 Å20.76 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4955 0 0 172 5127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195066
X-RAY DIFFRACTIONr_bond_other_d0.0040.024736
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.936865
X-RAY DIFFRACTIONr_angle_other_deg1.151310851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5625627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90724.089247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62715832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2381534
X-RAY DIFFRACTIONr_chiral_restr0.0860.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025811
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021211
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_it0.3811.2272532
X-RAY DIFFRACTIONr_mcbond_other0.3811.2272531
X-RAY DIFFRACTIONr_mcangle_it0.6891.8353151
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.271.2752534
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: 37052 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 94 -
Rwork0.303 2018 -
obs--91.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4967-0.17080.04124.11860.78671.36650.00370.020.1089-0.0543-0.0189-0.0268-0.1254-0.00430.01510.2124-0.0340.07540.0354-0.06320.1286-5.037149.732166.9491
21.20650.0855-0.18964.18751.19331.5964-0.01750.0321-0.06020.0856-0.0219-0.00140.18280.00840.03930.1927-0.0301-0.00750.029-0.05710.16025.463628.682827.0228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-14 - 346
2X-RAY DIFFRACTION2B-14 - 346

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