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- PDB-4mtm: Crystal structure of the tail fiber gp53 from Acinetobacter bauma... -

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Basic information

Entry
Database: PDB / ID: 4mtm
TitleCrystal structure of the tail fiber gp53 from Acinetobacter baumannii bacteriophage AP22
ComponentsPutative tail fiber protein
KeywordsSTRUCTURAL PROTEIN / Lectin fold / Tail fiber / receptor binding / bacterial cell surface / baseplate periphery
Function / homologyImmunoglobulin-like - #3940 / Immunoglobulin-like / Sandwich / Mainly Beta / BROMIDE ION / SULFITE ION / Putative tail fiber protein
Function and homology information
Biological speciesAcinetobacter bacteriophage AP22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.368 Å
AuthorsSycheva, L.V. / Shneider, M.M. / Leiman, P.G.
CitationJournal: Biorxiv / Year: 2019
Title: Crystal Structure of the putative tail fiber protein gp53 from the Acinetobacter baumannii bacteriophage AP22
Authors: Sycheva, L.V. / Shneider, M.M. / Popova, A.V. / Ziganshin, R.K. / Volozhantsev, N. / Miroshnikov, K.A. / Leiman, P.G.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,07028
Polymers17,1071
Non-polymers1,96327
Water2,684149
1
A: Putative tail fiber protein
hetero molecules

A: Putative tail fiber protein
hetero molecules

A: Putative tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,21184
Polymers51,3213
Non-polymers5,89081
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20650 Å2
ΔGint-140 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.200, 51.200, 302.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-324-

NA

21A-327-

SO3

31A-502-

HOH

41A-525-

HOH

51A-544-

HOH

DetailsThe biological assembly is a trimer generated from the monomer contained in the asymmetric unit using the following transformations: x, y, z; -y, x-y, z; and -x+y, -x, z.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative tail fiber protein


Mass: 17107.078 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues 108-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter bacteriophage AP22 (virus)
Gene: ORF53 / Plasmid: pEE3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: I2GUG0

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Non-polymers , 6 types, 176 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% PEG 4000, 0.225M lithium sulphate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2011
RadiationMonochromator: Bartels monochromator based on Si (111) crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.37→49.99 Å / Num. all: 62274 / Num. obs: 62273 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.3
Reflection shellResolution: 1.37→1.44 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXC/D/Emodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
SHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 1.368→19.719 Å / SU ML: 0.09 / σ(F): 0.04 / Phase error: 10.42 / Stereochemistry target values: Engh & Huber / Details: Br K-edge SAD
RfactorNum. reflection% reflectionSelection details
Rfree0.1317 1592 4.99 %Random
Rwork0.0993 ---
obs0.1009 31894 96.48 %-
all-33079 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.368→19.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 39 149 1201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131101
X-RAY DIFFRACTIONf_angle_d1.3171499
X-RAY DIFFRACTIONf_dihedral_angle_d11.347393
X-RAY DIFFRACTIONf_chiral_restr0.079181
X-RAY DIFFRACTIONf_plane_restr0.008187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.368-1.41210.20071300.15172472X-RAY DIFFRACTION88
1.4121-1.46260.15491330.11732627X-RAY DIFFRACTION93
1.4626-1.52110.14271360.09192649X-RAY DIFFRACTION94
1.5211-1.59030.14761450.08652710X-RAY DIFFRACTION96
1.5903-1.67410.11691450.07832703X-RAY DIFFRACTION97
1.6741-1.7790.10791460.07252750X-RAY DIFFRACTION97
1.779-1.91620.11421470.07022773X-RAY DIFFRACTION98
1.9162-2.10890.10711490.06832819X-RAY DIFFRACTION99
2.1089-2.41360.09341510.0762853X-RAY DIFFRACTION99
2.4136-3.0390.11961510.10842900X-RAY DIFFRACTION100
3.039-19.72140.16631590.13363046X-RAY DIFFRACTION100

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