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- PDB-6tud: Crystal structure of Y. pestis penicillin-binding protein 3 -

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Basic information

Entry
Database: PDB / ID: 6tud
TitleCrystal structure of Y. pestis penicillin-binding protein 3
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsCYTOSOLIC PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein
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 / proteolysis / plasma membrane
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 / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPankov, G. / Hunter, W.N. / Dawson, A.
CitationJournal: To Be Published
Title: The structure of penicillin-binding protein 3 from Yersinia pestis
Authors: Pankov, G.
History
DepositionJan 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
AAA: Peptidoglycan D,D-transpeptidase FtsI
BBB: Peptidoglycan D,D-transpeptidase FtsI


Theoretical massNumber of molelcules
Total (without water)119,1182
Polymers119,1182
Non-polymers00
Water48627
1
AAA: Peptidoglycan D,D-transpeptidase FtsI


Theoretical massNumber of molelcules
Total (without water)59,5591
Polymers59,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Peptidoglycan D,D-transpeptidase FtsI


Theoretical massNumber of molelcules
Total (without water)59,5591
Polymers59,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.800, 100.800, 314.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 59558.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ftsI, YPO0549 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0WJB8, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.47 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 1 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 6% gamma-PGA (Na+ form, LM) and 6% PEG8000) ...Details: 1 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 6% gamma-PGA (Na+ form, LM) and 6% PEG8000) Crystals were then dehydrated by replacing 50% of the reservoir solution with 50% PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9196 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 3→29.64 Å / Num. obs: 33546 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 50.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.071 / Net I/σ(I): 9.1
Reflection shellResolution: 3→3.15 Å / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4365 / CC1/2: 0.941 / Rpim(I) all: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SYN

6syn


Resolution: 3→29.64 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 26.209 / SU ML: 0.403 / Cross valid method: FREE R-VALUE / ESU R: 1.048 / ESU R Free: 0.398
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2764 1713 5.12 %
Rwork0.2439 --
all0.245 --
obs-33459 99.836 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.519 Å2
Baniso -1Baniso -2Baniso -3
1-7.716 Å20 Å20 Å2
2--7.716 Å20 Å2
3----15.432 Å2
Refinement stepCycle: LAST / Resolution: 3→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 0 27 7046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0137154
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176891
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.6429713
X-RAY DIFFRACTIONr_angle_other_deg1.0291.57215922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.56420.976338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.545151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8791557
X-RAY DIFFRACTIONr_chiral_restr0.0330.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021470
X-RAY DIFFRACTIONr_nbd_refined0.1670.21327
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.26505
X-RAY DIFFRACTIONr_nbtor_refined0.1460.23450
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.23290
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2151
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.225
X-RAY DIFFRACTIONr_nbd_other0.1840.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2220.25
X-RAY DIFFRACTIONr_mcbond_it1.5768.8453704
X-RAY DIFFRACTIONr_mcbond_other1.5738.8433703
X-RAY DIFFRACTIONr_mcangle_it2.86113.2524616
X-RAY DIFFRACTIONr_mcangle_other2.86113.2544617
X-RAY DIFFRACTIONr_scbond_it1.0699.0443450
X-RAY DIFFRACTIONr_scbond_other1.0699.0453451
X-RAY DIFFRACTIONr_scangle_it2.06913.5065097
X-RAY DIFFRACTIONr_scangle_other2.06913.5085098
X-RAY DIFFRACTIONr_lrange_it4.756103.8447540
X-RAY DIFFRACTIONr_lrange_other4.756103.8387540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0770.4831110.4282289X-RAY DIFFRACTION100
3.077-3.160.4271300.3872224X-RAY DIFFRACTION100
3.16-3.2510.3421100.3762179X-RAY DIFFRACTION99.9563
3.251-3.350.3721320.3512047X-RAY DIFFRACTION100
3.35-3.4580.2851070.332072X-RAY DIFFRACTION100
3.458-3.5780.3281100.2961974X-RAY DIFFRACTION100
3.578-3.7110.3741120.2931903X-RAY DIFFRACTION100
3.711-3.860.26870.261862X-RAY DIFFRACTION100
3.86-4.0280.305890.2321791X-RAY DIFFRACTION100
4.028-4.2210.26990.2081691X-RAY DIFFRACTION100
4.221-4.4440.22810.1881636X-RAY DIFFRACTION100
4.444-4.7070.2181040.1721528X-RAY DIFFRACTION100
4.707-5.0230.238670.1671485X-RAY DIFFRACTION100
5.023-5.4130.251700.1871377X-RAY DIFFRACTION100
5.413-5.910.259650.241293X-RAY DIFFRACTION100
5.91-6.5750.262570.2061165X-RAY DIFFRACTION100
6.575-7.5310.231660.1911051X-RAY DIFFRACTION100
7.531-9.0780.172470.153919X-RAY DIFFRACTION100
9.078-12.2750.172420.19743X-RAY DIFFRACTION100
12.275-29.640.299270.286517X-RAY DIFFRACTION99.8165

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