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- PDB-5w5p: Crystal structure of Acinetobacter baumannii phage AM24 tailspike... -

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Basic information

Entry
Database: PDB / ID: 5w5p
TitleCrystal structure of Acinetobacter baumannii phage AM24 tailspike protein
ComponentsTail fiber protein
KeywordsVIRAL PROTEIN / AM27 / Tailspike protein / Bacteriophage / capsular polysaccharide
Function / homologyTail fiber protein
Function and homology information
Biological speciesAcinetobacter phage AM24 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.429 Å
AuthorsPlattner, M. / Shneider, M.M. / Leiman, P.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Ecole polytechnique federale de Lausanne0577-1 Switzerland
CitationJournal: To be Published
Title: Crystal structure of Acinetobacter baumannii phage AM24 tailspike protein
Authors: Plattner, M. / Shneider, M.M. / Leiman, P.G.
History
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4653
Polymers67,3341
Non-polymers1312
Water4,522251
1
A: Tail fiber protein
hetero molecules

A: Tail fiber protein
hetero molecules

A: Tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,3969
Polymers202,0033
Non-polymers3926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area27710 Å2
ΔGint-290 kcal/mol
Surface area53060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.657, 100.657, 307.836
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-905-

HOH

21A-960-

HOH

31A-1013-

HOH

41A-1026-

HOH

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Components

#1: Protein Tail fiber protein


Mass: 67334.359 Da / Num. of mol.: 1 / Fragment: UNP residues 230-848
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter phage AM24 (virus) / Production host: Escherichia coli B (bacteria) / Strain (production host): 834 / References: UniProt: A0A1J0MGR2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 38% PEG1000, 120 mM magnesium sulfate, 100 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.429→50 Å / Num. obs: 64571 / % possible obs: 97.9 % / Redundancy: 20 % / Net I/σ(I): 21.04
Reflection shellHighest resolution: 2.429 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.429→47.836 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.71
RfactorNum. reflection% reflection
Rfree0.2171 3243 5.03 %
Rwork0.1802 --
obs0.182 64470 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.429→47.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 2 251 4859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034690
X-RAY DIFFRACTIONf_angle_d0.5546366
X-RAY DIFFRACTIONf_dihedral_angle_d6.5452735
X-RAY DIFFRACTIONf_chiral_restr0.045727
X-RAY DIFFRACTIONf_plane_restr0.003825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4286-2.46490.3126800.31331467X-RAY DIFFRACTION53
2.4649-2.50340.31691410.27252680X-RAY DIFFRACTION100
2.5034-2.54440.29121420.26212703X-RAY DIFFRACTION100
2.5444-2.58830.27511470.2562750X-RAY DIFFRACTION100
2.5883-2.63540.29661430.24262702X-RAY DIFFRACTION100
2.6354-2.68610.29721400.23552702X-RAY DIFFRACTION100
2.6861-2.74090.21731450.22592715X-RAY DIFFRACTION100
2.7409-2.80050.24741470.21862764X-RAY DIFFRACTION100
2.8005-2.86560.24451470.22662720X-RAY DIFFRACTION100
2.8656-2.93730.26421430.22582657X-RAY DIFFRACTION100
2.9373-3.01670.29511500.22572738X-RAY DIFFRACTION100
3.0167-3.10540.27741440.22172704X-RAY DIFFRACTION100
3.1054-3.20560.25451420.20722736X-RAY DIFFRACTION100
3.2056-3.32020.24051420.20372696X-RAY DIFFRACTION100
3.3202-3.45310.22581490.19212742X-RAY DIFFRACTION100
3.4531-3.61020.21751370.16882718X-RAY DIFFRACTION100
3.6102-3.80040.17631440.15622708X-RAY DIFFRACTION100
3.8004-4.03840.17911450.14642731X-RAY DIFFRACTION100
4.0384-4.35010.16881430.13422715X-RAY DIFFRACTION100
4.3501-4.78750.1821440.12512705X-RAY DIFFRACTION99
4.7875-5.47930.16581400.14212720X-RAY DIFFRACTION100
5.4793-6.90010.1881410.16512716X-RAY DIFFRACTION100
6.9001-47.84540.21961470.17752738X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.66030.29321.40231.53651.29492.88880.0143-0.3055-0.05040.1815-0.01670.05050.1574-0.3088-0.00190.5525-0.02230.0560.57060.060.436938.197526.191547.4937
20.6444-0.1592-0.1520.41250.28662.13870.0668-0.0178-0.09130.09280.04620.04470.1604-0.2337-0.11570.417-0.0248-0.01670.40910.04180.428736.613918.87915.8157
30.5638-0.1193-0.1070.5417-0.12761.27970.05960.24550.108-0.12330.0275-0.1298-0.16320.1246-0.08780.5059-0.01130.02420.52410.00310.397256.460135.9113-39.7236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 117 )
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 396 )
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 619 )

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