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- PDB-3f8v: Evaulaution at Atomic Resolution of the Role of Strain in Destabi... -

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Basic information

Entry
Database: PDB / ID: 3f8v
TitleEvaulaution at Atomic Resolution of the Role of Strain in Destabilizing the Temperature Sensitive T4 Lysozyme Mutant Arg96-->His
ComponentsLysozyme
KeywordsHYDROLASE / Antimicrobial / Bacteriolytic enzyme / Glycosidase / T4 lysozyme / bond angle strain / rotamer strain / temperature sensitive mutant
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-HYDROXYETHYL DISULFIDE / : / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.08 Å
AuthorsMooers, B.H.M. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 2009
Title: Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 --> His.
Authors: Mooers, B.H. / Tronrud, D.E. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 2009
Title: Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme.
Authors: Mooers, B.H. / Baase, W.A. / Wray, J.W. / Matthews, B.W.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0267
Polymers18,6431
Non-polymers3826
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.123, 60.123, 95.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme / / E.C.3.2.1.17 / Lysis protein / Muramidase / Endolysin


Mass: 18643.420 Da / Num. of mol.: 1 / Mutation: R96H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: gene e / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme

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Non-polymers , 6 types, 248 molecules

#2: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 2 M Na/K Phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 8, 1999
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.08→17.9 Å / Num. all: 85136 / Num. obs: 72503 / % possible obs: 99.5 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 10.4 Å2 / Rsym value: 0.038 / Net I/σ(I): 20.3
Reflection shellResolution: 1.08→1.14 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 11790 / Rsym value: 0.23 / % possible all: 99.5

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Processing

Software
NameClassification
MAR345dtbdata collection
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: l163, wild type T4 lysozyme at 1.7 Angstroms and room temp.

Resolution: 1.08→17.9 Å / Num. parameters: 14302 / Num. restraintsaints: 17026 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 5%
RfactorNum. reflection% reflectionSelection details
Rfree0.163 4242 5 %RANDOM
Rwork0.1289 ---
all0.1435 85136 --
obs0.138 72503 99.5 %-
Refine analyzeLuzzati coordinate error obs: 0.06 Å / Num. disordered residues: 19 / Occupancy sum hydrogen: 1264.5 / Occupancy sum non hydrogen: 1535.05
Refinement stepCycle: LAST / Resolution: 1.08→17.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 17 257 1589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0237
X-RAY DIFFRACTIONs_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.038
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.1
LS refinement shellResolution: 1.08→1.14 Å /
Num. reflection% reflection
obs11790 96.58 %

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