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- PDB-1qrb: PLASTICITY AND STERIC STRAIN IN A PARALLEL BETA-HELIX: RATIONAL M... -

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Basic information

Entry
Database: PDB / ID: 1qrb
TitlePLASTICITY AND STERIC STRAIN IN A PARALLEL BETA-HELIX: RATIONAL MUTATIONS IN P22 TAILSPIKE PROTEIN
ComponentsPROTEIN (TAILSPIKE-PROTEIN)
KeywordsVIRAL PROTEIN / BETA-HELIX
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 / metabolic process / 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 / Resolution: 2 Å
AuthorsSchuler, B. / Furst, F. / Osterroth, F. / Steinbacher, S. / Huber, R. / Seckler, R.
CitationJournal: Proteins / Year: 2000
Title: Plasticity and steric strain in a parallel beta-helix: rational mutations in the P22 tailspike protein.
Authors: Schuler, B. / Furst, F. / Osterroth, F. / Steinbacher, S. / Huber, R. / Seckler, R.
History
DepositionJun 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (TAILSPIKE-PROTEIN)


Theoretical massNumber of molelcules
Total (without water)60,3111
Polymers60,3111
Non-polymers00
Water3,927218
1
A: PROTEIN (TAILSPIKE-PROTEIN)

A: PROTEIN (TAILSPIKE-PROTEIN)

A: PROTEIN (TAILSPIKE-PROTEIN)


Theoretical massNumber of molelcules
Total (without water)180,9343
Polymers180,9343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area27600 Å2
ΔGint-115 kcal/mol
Surface area48180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.9, 120.9, 120.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number198
Space group name H-MP213

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Components

#1: Protein PROTEIN (TAILSPIKE-PROTEIN) / TSP


Mass: 60311.340 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT / Mutation: T326F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / References: UniProt: P12528
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 1M AMMONIUM SULPHATE 0.1 M SODIUM PHOSPHATE, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: Steinbacher, S., (1994) Science, 265, 383.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Mammonium sulfate1reservoir
20.1 Msodium phosphate1reservoir
310 mg/mlprotein1drop
410 mMHEPES1drop
51.5 Mammonium sulfate1drop
60.1 Msodium phosphate1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 38358 / Num. obs: 38358 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.233 / % possible all: 79.7
Reflection
*PLUS
Num. measured all: 167323
Reflection shell
*PLUS
% possible obs: 79.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection
Rwork0.156 -
all0.156 37769
obs0.156 37769
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4119 0 0 218 4337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.737
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.64
X-RAY DIFFRACTIONx_dihedral_angle_deg26.91
X-RAY DIFFRACTIONx_improper_angle_deg1.29

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