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- PDB-4xlc: Tailspike protein double mutant D339N/E372A of E. coli bacterioph... -

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Basic information

Entry
Database: PDB / ID: 4xlc
TitleTailspike protein double mutant D339N/E372A of E. coli bacteriophage HK620
ComponentsTail spike protein
KeywordsVIRAL PROTEIN / beta helix / protein-carbohydrate complex / pectin lyase fold
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component / metal ion binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #250 / Phage spike trimer 2 / Phage spike trimer / HK620, Tail spike protein, C-terminal / Hk620 tailspike protein, N-terminal domain-like / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Arc Repressor Mutant, subunit A / Single-stranded right-handed beta-helix, Pectin lyase-like ...Elongation Factor Tu (Ef-tu); domain 3 - #250 / Phage spike trimer 2 / Phage spike trimer / HK620, Tail spike protein, C-terminal / Hk620 tailspike protein, N-terminal domain-like / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Arc Repressor Mutant, subunit A / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Elongation Factor Tu (Ef-tu); domain 3 / Helix non-globular / Special / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Tail spike protein
Similarity search - Component
Biological speciesEnterobacteria phage HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsGohlke, U. / Broeker, N.K. / Heinemann, U. / Seckler, R. / Barbirz, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationBA 4046/1-1 Germany
Citation
Journal: to be published
Title: Enthalpic cost of water removal from a hydrophobic glucose binding cavity on HK620 tailspike protein.
Authors: Gohlke, U. / Broeker, N.K. / Kunstmann, S. / Santer, M. / Heinemann, U. / Lipowski, R. / Seckler, R. / Barbirz, S.
#1: Journal: Glycobiology / Year: 2013
Title: Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity.
Authors: Broeker, N.K. / Gohlke, U. / Mueller, J.J. / Uetrecht, C. / Heinemann, U. / Seckler, R. / Barbirz, S.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr2_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9608
Polymers64,5311
Non-polymers4287
Water9,998555
1
A: Tail spike protein
hetero molecules

A: Tail spike protein
hetero molecules

A: Tail spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,87924
Polymers193,5943
Non-polymers1,28521
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 area24530 Å2
ΔGint-138 kcal/mol
Surface area50320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.176, 74.176, 174.695
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1440-

HOH

21A-1454-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y+1,x-y,z and -x+y+1,-x+1,z.

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Components

#1: Protein Tail spike protein


Mass: 64531.246 Da / Num. of mol.: 1 / Fragment: head binding, unp residues 112-710 / Mutation: D339N, E372A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK620 (virus) / Plasmid: pET11d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9AYY6
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 3.5 M Sodiumformate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 8, 2012 / Details: mirrors
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.85→43.67 Å / Num. obs: 48154 / % possible obs: 99.6 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Net I/σ(I): 15.7 / Num. measured all: 292708
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.85-1.895.90.85921641427840.6650.38294.5
9.07-43.674.90.02151.3237848810.0198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.94 Å43.67 Å
Translation5.94 Å43.67 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
ARPmodel building
Cootmodel building
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AVZ

4avz


Resolution: 1.85→43.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1692 / WRfactor Rwork: 0.1221 / FOM work R set: 0.8573 / SU B: 6.76 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1278 / SU Rfree: 0.1268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2407 5 %RANDOM
Rwork0.1479 45746 --
obs0.1505 48154 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.43 Å2 / Biso mean: 22.597 Å2 / Biso min: 11.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å2-0 Å2
2--0.76 Å20 Å2
3----2.48 Å2
Refinement stepCycle: final / Resolution: 1.85→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4543 0 27 555 5125
Biso mean--30.66 31.79 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194775
X-RAY DIFFRACTIONr_bond_other_d0.0010.024260
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9166523
X-RAY DIFFRACTIONr_angle_other_deg0.87439742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1245624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62524.386228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53815672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7861523
X-RAY DIFFRACTIONr_chiral_restr0.140.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021236
X-RAY DIFFRACTIONr_mcbond_it0.6671.0232462
X-RAY DIFFRACTIONr_mcbond_other0.6681.0232463
X-RAY DIFFRACTIONr_mcangle_it0.9741.5313096
LS refinement shellResolution: 1.852→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 171 -
Rwork0.243 3230 -
all-3401 -
obs--96.15 %
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)
10.5017-2.1042.734418.16411.266434.8570.25340.1101-0.1058-1.57710.09320.68570.18840.028-0.34660.5068-0.0314-0.11311.09350.18610.351133.613925.8607-24.1611
21.39482.0535-0.74016.3832-2.05292.7979-0.05370.25330.0076-0.3617-0.06540.0890.0964-0.02110.11910.16680.0246-0.0150.2224-0.02540.108531.00218.5567-7.6568
30.86740.0012-0.16721.10750.32663.0368-0.12180.1110.0761-0.0338-0.0583-0.0291-0.3608-0.04010.18010.20140.0142-0.08030.11510.03470.121534.867441.688810.1929
414.6755-8.1047-3.551813.05442.79165.14510.14380.22070.3518-0.0863-0.35810.5189-0.5516-0.6670.21430.20740.0624-0.06170.3410.01080.195218.448442.425221.9212
51.24980.15560.14930.42750.03861.5169-0.06190.08120.1037-0.0959-0.07470.0189-0.2968-0.00730.13660.11330.0078-0.05360.03720.01490.100436.20239.771629.9348
63.4142-0.4904-0.00670.45360.27551.9896-0.00890.1010.1666-0.0981-0.11610.1268-0.3169-0.29220.1250.09650.0434-0.04470.0736-0.01560.118728.257439.51942.9896
71.87420.4252-0.2511.03990.25790.9249-0.0460.00960.1669-0.0531-0.01040.0183-0.2052-0.01480.05640.05260.0023-0.02690.00160.00880.082737.964439.159252.1826
812.47185.6281.91929.3711-7.629611.1423-0.4891-0.30771.53230.58020.03930.2442-1.384-0.09130.44990.6455-0.07470.18280.2027-0.27090.703636.176250.331360.0216
90.962-0.10420.04630.1617-0.1010.6634-0.0156-0.06680.10540.0544-0.0208-0.0325-0.06960.03750.03650.0257-0.0057-0.01040.0145-0.00620.132938.841137.569369.9914
101.0413-0.19371.01390.1211-0.14391.97640.0315-0.0028-0.00830.0422-0.0067-0.0406-0.10730.0821-0.02480.0586-0.016-0.00560.0516-0.01090.155541.678830.570893.1471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A111 - 115
2X-RAY DIFFRACTION2A116 - 148
3X-RAY DIFFRACTION3A149 - 250
4X-RAY DIFFRACTION4A251 - 259
5X-RAY DIFFRACTION5A260 - 392
6X-RAY DIFFRACTION6A393 - 438
7X-RAY DIFFRACTION7A439 - 524
8X-RAY DIFFRACTION8A525 - 532
9X-RAY DIFFRACTION9A533 - 636
10X-RAY DIFFRACTION10A637 - 709

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