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- PDB-6hzo: Apo structure of TP domain from Haemophilus influenzae Penicillin... -

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Basic information

Entry
Database: PDB / ID: 6hzo
TitleApo structure of TP domain from Haemophilus influenzae Penicillin-Binding Protein 3
ComponentsFtsI
KeywordsPEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane => GO:0005886
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / DD-peptidase/beta-lactamase superfamily / Beta-lactamase / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesHaemophilus influenzae (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsBellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)grant.MR/P007503/1 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam ...Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam Target-Mediated Resistance.
Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G.
History
DepositionOct 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FtsI
B: FtsI
C: FtsI
D: FtsI


Theoretical massNumber of molelcules
Total (without water)141,4024
Polymers141,4024
Non-polymers00
Water39622
1
A: FtsI


Theoretical massNumber of molelcules
Total (without water)35,3501
Polymers35,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FtsI


Theoretical massNumber of molelcules
Total (without water)35,3501
Polymers35,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FtsI


Theoretical massNumber of molelcules
Total (without water)35,3501
Polymers35,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FtsI


Theoretical massNumber of molelcules
Total (without water)35,3501
Polymers35,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.014, 93.632, 95.830
Angle α, β, γ (deg.)90.00, 95.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FtsI


Mass: 35350.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (unknown) / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: P45059*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3,350 and 0.2 M KNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.44→95.4 Å / Num. obs: 33806 / % possible obs: 91.8 % / Redundancy: 4.4 % / Rrim(I) all: 0.086 / Net I/σ(I): 12.6
Reflection shellResolution: 2.44→2.69 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
DIALSdata reduction
AutoPROCdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BJP
Resolution: 2.44→95.4 Å / Cor.coef. Fo:Fc: 0.93 / SU B: 12.234 / SU ML: 0.254 / Cross valid method: FREE R-VALUE / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.22374 --
obs0.22374 33799 67.78 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.372 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å2-0.09 Å2
2--0.22 Å20 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 2.44→95.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8705 0 0 22 8727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138830
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178653
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.65211952
X-RAY DIFFRACTIONr_angle_other_deg1.1921.57719981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35551121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.24720.998431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.758151538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9381576
X-RAY DIFFRACTIONr_chiral_restr0.0660.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029783
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021809
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_it5.2396.2674532
X-RAY DIFFRACTIONr_mcbond_other5.2396.2664531
X-RAY DIFFRACTIONr_mcangle_it8.1779.3725637
X-RAY DIFFRACTIONr_mcangle_other8.1779.3735638
X-RAY DIFFRACTIONr_scbond_it5.8867.0324298
X-RAY DIFFRACTIONr_scbond_other5.8857.0334299
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.42710.2476316
X-RAY DIFFRACTIONr_long_range_B_refined13.0474.5279742
X-RAY DIFFRACTIONr_long_range_B_other13.03974.5349742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.441→2.504 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.328 67 -
obs--1.84 %

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