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- PDB-1tvf: Crystal Structure of penicillin-binding protein 4 (PBP4) from Sta... -

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Basic information

Entry
Database: PDB / ID: 1tvf
TitleCrystal Structure of penicillin-binding protein 4 (PBP4) from Staphylococcus aureus
Componentspenicillin binding protein 4
KeywordsPENICILLIN BINDING / Structural Genomics / NYSGXRC TARGET / T72 / PBP4 / SAV0642 / SA0598 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / response to antibiotic / proteolysis / membrane
Similarity search - Function
Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain superfamily / Domain of unknown function (DUF1958) / 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 / Spermidine Synthase; Chain: A, domain 2 / Beta-lactamase, class-A ...Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain superfamily / Domain of unknown function (DUF1958) / 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 / Spermidine Synthase; Chain: A, domain 2 / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Pencillin binding protein 4 / Penicillin binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS, MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRajashankar, K.R. / Ray, S.S. / Bonanno, J.B. / Pinho, M. / Tomasz, A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of penicillin-binding protein 4 (PBP4) from Staphylococcus aureus
Authors: Rajashankar, K.R. / Ray, S.S. / Bonanno, J.B. / Pinho, M. / Tomasz, A. / Burley, S.K.
History
DepositionJun 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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 / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: penicillin binding protein 4
B: penicillin binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9579
Polymers82,4772
Non-polymers4807
Water14,070781
1
A: penicillin binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5275
Polymers41,2381
Non-polymers2884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: penicillin binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4314
Polymers41,2381
Non-polymers1923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.713, 140.189, 145.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsEach monomer seem to form a biological unit.

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Components

#1: Protein penicillin binding protein 4 / PBP4


Mass: 41238.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: PBP4 / Plasmid: PET T7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q53613, UniProt: Q57540*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.58 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 24% PEG 4000, 100mM citrate buffer, 200mM Ammonium Sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.98
SYNCHROTRONNSLS X9A21.25
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.251
ReflectionResolution: 2→30 Å / Num. all: 67865 / Num. obs: 67865 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 9.5 Å2 / Rsym value: 0.058 / Net I/σ(I): 17.1
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.196 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SIRAS, MOLECULAR REPLACEMENT
Starting model: Arp/Warp autobuilt model using phases from two Ta6Br12 clusters and a poor molecular replacement solution. MR was carried out using a model derived from PDB entry 1HD8, which is a ...Starting model: Arp/Warp autobuilt model using phases from two Ta6Br12 clusters and a poor molecular replacement solution. MR was carried out using a model derived from PDB entry 1HD8, which is a mutant of PBP5, sharing ~26% identity with PBP4 over a 245 residue range. Phase combination with MR solution was necessary, as Ta6Br12 clusters occupied positions on the symmetry planes resulting in centrosymmetric phases and hence uninterpretable maps.

1hd8


Resolution: 2→23.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 425919.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Unidentified electron density is observed near the active site.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3423 5.1 %RANDOM
Rwork0.166 ---
obs0.166 67366 98.4 %-
all-67366 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.8694 Å2 / ksol: 0.368462 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.66 Å20 Å20 Å2
2--2.23 Å20 Å2
3---1.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→23.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 43 781 6620
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.228 548 5 %
Rwork0.187 10502 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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