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- PDB-5mu4: Tail Tubular Protein A of Klebsiella pneumoniae bacteriophage KP32 -

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Basic information

Entry
Database: PDB / ID: 5mu4
TitleTail Tubular Protein A of Klebsiella pneumoniae bacteriophage KP32
ComponentsTail tubular protein A
KeywordsVIRAL PROTEIN / tail tubular protein / bacteriophage / exopolysaccharide depolymerase / antibacterial activity
Function / homologyTail tubular protein Gp11 / Tail tubular protein / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion component / Tail tubular protein A
Function and homology information
Biological speciesKlebsiella phage KP32 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPyra, A. / Brzozowska, E. / Pawlik, K. / Dauter, M. / Dauter, Z. / Gamian, A.
CitationJournal: Sci Rep / Year: 2017
Title: Tail tubular protein A: a dual-function tail protein of Klebsiella pneumoniae bacteriophage KP32.
Authors: Pyra, A. / Brzozowska, E. / Pawlik, K. / Gamian, A. / Dauter, M. / Dauter, Z.
History
DepositionJan 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Data collection / Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail tubular protein A
B: Tail tubular protein A
C: Tail tubular protein A
D: Tail tubular protein A


Theoretical massNumber of molelcules
Total (without water)89,1274
Polymers89,1274
Non-polymers00
Water14,250791
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-22 kcal/mol
Surface area34920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.320, 138.320, 102.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Tail tubular protein A


Mass: 22281.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage KP32 (virus) / Gene: 31
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D1L2W4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 35% Tacsimate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.9792
SYNCHROTRONAPS 22-ID20.9763
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDOct 13, 2014
RAYONIX MX-3002CCDOct 13, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97631
ReflectionResolution: 1.9→30 Å / Num. obs: 87540 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.04 / Rrim(I) all: 0.113 / Χ2: 0.933 / Net I/σ(I): 9.4 / Num. measured all: 718685
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.9-1.936.743620.6430.7880.83199.8
1.93-1.976.843430.7060.6460.85299.9
1.97-2.01743640.8070.5490.84399.9
2.01-2.057.143740.8460.4470.851100
2.05-2.097.143430.8940.3430.88499.90.8630.93
2.09-2.147.243340.9360.2630.8699.90.6650.716
2.14-2.197.243930.9540.2190.87899.90.5510.594
2.19-2.257.243370.9650.1830.8831000.4610.496
2.25-2.327.243600.9730.1380.881000.3470.374
2.32-2.397.244020.9770.1150.8521000.290.312
2.39-2.487.243540.9790.0980.861000.2460.265
2.48-2.587.343710.9830.0750.8431000.1890.204
2.58-2.77.343720.9850.0610.8491000.1550.167
2.7-2.847.343770.9890.0510.8661000.1290.138
2.84-3.02943890.990.0430.9351000.1250.132
3.02-3.2511.143780.990.041.1011000.1260.133
3.25-3.5711.243940.9910.0361.1961000.1140.12
3.57-4.0911.243920.9890.0311.0851000.0970.102
4.09-5.151144170.9940.0250.9061000.0770.081
5.15-3010.644840.9870.0280.99699.80.0810.086

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data collection
HKL-2000data reduction
SHELXDEphasing
HKL-2000data scaling
HKLdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.403 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1650 2 %RANDOM
Rwork0.1831 ---
obs0.1841 81538 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 112.67 Å2 / Biso mean: 28.628 Å2 / Biso min: 8.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.9→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5861 0 0 791 6652
Biso mean---37.46 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195995
X-RAY DIFFRACTIONr_bond_other_d0.0020.025446
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.948123
X-RAY DIFFRACTIONr_angle_other_deg1.111312492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4625751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13924.537313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46815968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7261546
X-RAY DIFFRACTIONr_chiral_restr0.1480.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021450
LS refinement shellResolution: 1.903→1.953 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 76 -
Rwork0.294 3292 -
all-3368 -
obs--52.34 %

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