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- PDB-1sdn: CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN... -

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Basic information

Entry
Database: PDB / ID: 1sdn
TitleCRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN-BINDING PROTEIN 5 MODIFIED BY MERCURY
ComponentsPenicillin-binding protein 5
KeywordsHYDROLASE / PEPTIDOGLYCAN SYNTHESIS / PENICLLIN-BINDING PROTEIN / DD-CARBOXYPEPTIDASE
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 / beta-lactamase activity / regulation of cell shape ...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 / beta-lactamase activity / regulation of cell shape / outer membrane-bounded periplasmic space / cell division / 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
: / D-alanyl-D-alanine carboxypeptidase DacA / D-alanyl-D-alanine carboxypeptidase DacA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / REFINEMENT / Resolution: 2.5 Å
AuthorsNicola, G. / Nicholas, R.A. / Davies, C.
Citation
Journal: Biochem.J. / Year: 2005
Title: A large displacement of the SXN motif of Cys115-modified penicillin-binding protein 5 from Escherichia coli.
Authors: Nicola, G. / Fedarovich, A. / Nicholas, R.A. / Davies, C.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure of a Deacylation-Defective Mutant of Penicllin-Binding Protein at 2.3 A Resolution
Authors: Davies, C. / White, S.W. / Nicholas, R.A.
#2: Journal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Wild-Type Penicillin-Binding Protein 5 from Escherichia Coli: Implications for Deacylation of the Acyl-Enzyme Complex
Authors: Nicholas, R.A. / Krings, S. / Tomberg, J. / Nicola, G. / Davies, C.
History
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5'. TO PRODUCE SPBP5 CODONS ...SEQUENCE THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5'. TO PRODUCE SPBP5 CODONS CORRESPONDING TO THE LAST 17 AMINO ACID RESIDUES WERE REMOVED BUT AN ADDITIONAL SIX AMINO ACIDS (GDPVID) WERE ADDED DUE TO READ THROUGH TO THE STOP CODON. NONE OF THESE NON-NATIVE RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY MAP. THE FIRST 29 AMINO ACIDS OF THE PROTEIN ENCODED BY THE OPEN READING FRAME REPRESENT THE SIGNAL SEQUENCE, WHICH IS REMOVED DURING MATURATION AND TRANSPORT TO THE PERIPLASMIC SPACE. THESE RESIDUES ARE NOT PRESENT IN THIS CONSTRUCT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1002
Polymers39,8991
Non-polymers2011
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.7, 50.7, 140.3
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Penicillin-binding protein 5 / D-alanyl-D-alanine carboxypeptidase fraction A / DD-peptidase / DD-carboxypeptidase / PBP-5


Mass: 39899.152 Da / Num. of mol.: 1 / Mutation: G105D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DACA, PFV, B0632, C0722, Z0777, ECS0670 / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061
References: UniProt: P04287, UniProt: P0AEB2*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.77 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24% (w/v) polyethylene glycol 8000, 50mM sodium citrate, 100mM magnesium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2000H / Detector: IMAGE PLATE / Date: Aug 20, 1998 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25.4 Å / Num. all: 13482 / Num. obs: 13482 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.53 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.2
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 4.4 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
NONIUSdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: REFINEMENT
Starting model: PDB ENTRY 1HD8

1hd8


Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.1 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.494 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24142 688 5 %RANDOM
Rwork0.17113 ---
all0.1744 13044 --
obs0.17447 13044 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.141 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å20 Å2
2---0.7 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 1 46 2726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222726
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9563680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065345
X-RAY DIFFRACTIONr_chiral_restr0.0850.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022049
X-RAY DIFFRACTIONr_nbd_refined0.1960.21017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.22
X-RAY DIFFRACTIONr_mcbond_it0.7281.51714
X-RAY DIFFRACTIONr_mcangle_it1.40822747
X-RAY DIFFRACTIONr_scbond_it1.86531012
X-RAY DIFFRACTIONr_scangle_it3.2674.5933
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 49
Rwork0.203 929

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