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- PDB-2vfn: Low Temperature Structure of P22 Tailspike Protein Fragment (109-... -

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Basic information

Entry
Database: PDB / ID: 2vfn
TitleLow Temperature Structure of P22 Tailspike Protein Fragment (109-666), Mutant V125A
ComponentsBIFUNCTIONAL TAIL PROTEIN
KeywordsHYDROLASE / P22 TAILSPIKE PROTEIN / SALMONELLA BACTERIOPHAGE P22 / PROTEIN FOLDING / PROTEIN STABILITY / RIGHT-HANDED PARALLEL BETA-HELIX / LATE PROTEIN / ENDOGLYCOSIDASE
Function / homology
Function and homology information


endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell
Similarity search - Function
Pectate Lyase C-like - #20 / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectate Lyase C-like / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesENTEROBACTERIA PHAGE P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBecker, M. / Mueller, J.J. / Heinemann, U. / Seckler, R.
Citation
Journal: To be Published
Title: Side-Chain Stacking and Beta-Helix Stability in P22 Tailspike Protein
Authors: Becker, M. / Mueller, J.J. / Weikl, T. / Heinemann, U. / Seckler, R.
#1: Journal: Proteins: Struct.,Funct., Genet. / Year: 2000
Title: Plasticity and Steric Strain in a Parallel Beta-Helix: Rational Mutations in the P22 Tailspike Protein
Authors: Schuler, B. / Fuerst, F. / Osterroth, F. / Steinbacher, S. / Huber, R. / Seckler, R.
History
DepositionNov 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIFUNCTIONAL TAIL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,26213
Polymers60,2051
Non-polymers1,05712
Water14,484804
1
A: BIFUNCTIONAL TAIL PROTEIN
hetero molecules

A: BIFUNCTIONAL TAIL PROTEIN
hetero molecules

A: BIFUNCTIONAL TAIL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,78739
Polymers180,6163
Non-polymers3,17136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area32510 Å2
ΔGint-163.8 kcal/mol
Surface area62470 Å2
MethodPQS
Unit cell
Length a, b, c (Å)120.437, 120.437, 120.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1678-

CA

21A-2155-

HOH

31A-2228-

HOH

41A-2393-

HOH

51A-2407-

HOH

61A-2553-

HOH

71A-2575-

HOH

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Components

#1: Protein BIFUNCTIONAL TAIL PROTEIN / P22 TAILSPIKE PROTEIN / MUTANT V125A / LATE PROTEIN GP9 / TAILSPIKE-PROTEIN / TSP / ...P22 TAILSPIKE PROTEIN / MUTANT V125A / LATE PROTEIN GP9 / TAILSPIKE-PROTEIN / TSP / ENDORHAMNOSIDASE / ENDO-1 / 3-ALPHA-L-RHAMNOSIDASE


Mass: 60205.238 Da / Num. of mol.: 1 / Fragment: RESIDUES 110-667 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN IS LACKING THE N-TERMINAL HEAD-BINDING DOMAIN
Source: (gene. exp.) ENTEROBACTERIA PHAGE P22 (virus) / Plasmid: P125ADN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83
References: UniProt: P12528, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 126 TO ALA
Sequence detailsGLY513 IN THE SWISSPROT ENTRY WAS CORRECTED IN THE SEQUENCE TO SER513 WHICH IS ALSO PRESENT IN THE ...GLY513 IN THE SWISSPROT ENTRY WAS CORRECTED IN THE SEQUENCE TO SER513 WHICH IS ALSO PRESENT IN THE PARENT WILD-TYPE DNA

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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: 2.44 Å3/Da / Density % sol: 49.49 %
Description: FOR REFINEMENT REFLECTIONS IN THE CORNERS OF THE IMAGE PLATE WERE USED ADDITIONALLY, 1.5-1.59 A RESOLUTION, COMPETENESS 42.6 PERCENT, REDUNDANCY 1.7, RSYM 0.101, I DIVIDED BY SIGMA(I) 6.8
Crystal growpH: 10
Details: DROP: 2 MICROLITER 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0, PLUS 3.3 MICROLITER, 10 MG/ML PROTEIN SOLUTION IN 10 MM HEPES, PH 7.0; RESERVOIR: 750 MICOLITER 1.0 M AMMONIUM ...Details: DROP: 2 MICROLITER 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0, PLUS 3.3 MICROLITER, 10 MG/ML PROTEIN SOLUTION IN 10 MM HEPES, PH 7.0; RESERVOIR: 750 MICOLITER 1.0 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.92018
DetectorType: MARRESEARCH / Detector: CCD / Date: May 2, 2007 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92018 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 76620 / % possible obs: 98.1 % / Redundancy: 12.9 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.9
Reflection shellResolution: 1.59→1.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 10.2 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VFQ

2vfq


Resolution: 1.5→49.15 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.946 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.155 4162 5 %RANDOM
Rwork0.127 ---
obs0.128 79072 89.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.84 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 66 804 5074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224544
X-RAY DIFFRACTIONr_bond_other_d0.0010.023061
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9646155
X-RAY DIFFRACTIONr_angle_other_deg0.91637497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69924.573199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61115747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7271524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02903
X-RAY DIFFRACTIONr_nbd_refined0.190.2749
X-RAY DIFFRACTIONr_nbd_other0.1960.23160
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22130
X-RAY DIFFRACTIONr_nbtor_other0.0790.22318
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2510
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.2143
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.287
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.54822939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07334574
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.35941853
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.65761578
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.55 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.225 138
Rwork0.172 2632

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