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- PDB-3fi5: Crystal Structure of T4 Lysozyme Mutant R96W -

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Basic information

Entry
Database: PDB / ID: 3fi5
TitleCrystal Structure of T4 Lysozyme Mutant R96W
ComponentsLysozyme
KeywordsHYDROLASE / Antimicrobial / Bacteriolytic enzyme / Glycosidase / T4 lysozyme / electrostatics / strain / protein stability
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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsMooers, B.H.M. / Matthews, B.W.
Citation
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.
#1: 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.
History
DepositionDec 11, 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: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
C: Lysozyme
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,03712
Polymers74,7664
Non-polymers2718
Water17,925995
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8104
Polymers18,6911
Non-polymers1193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7503
Polymers18,6911
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7503
Polymers18,6911
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7272
Polymers18,6911
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.800, 56.110, 85.240
Angle α, β, γ (deg.)90.00, 106.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18691.482 Da / Num. of mol.: 4 / Mutation: R96W
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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 995 / 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: 2.26 Å3/Da / Density % sol: 45.66 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 29, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.53→18.804 Å / Num. all: 101134 / Num. obs: 92759 / % possible obs: 70.2 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 12.42 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 19.96
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 5.15 / Num. unique all: 3111 / Rsym value: 0.195 / % possible all: 41.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LW9

1lw9


Resolution: 1.53→18.804 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 2319 2.5 %random
Rwork0.1938 ---
obs0.1955 92759 91.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.343 Å2 / ksol: 0.408 e/Å3
Refinement stepCycle: LAST / Resolution: 1.53→18.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 7 1063 6606
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.863
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.53-1.56120.25361260.1997493585
1.5612-1.59510.31251320.1947512689
1.5951-1.63220.26241360.1914529592
1.6322-1.6730.26081390.1765543094
1.673-1.71820.26221420.1641552996
1.7182-1.76880.2331430.159558997
1.7688-1.82580.25131460.1598567398
1.8258-1.8910.29631430.195558496
1.891-1.96660.2691440.2131561898
1.9666-2.0560.25041480.179575999
2.056-2.16430.2351470.15895767100
2.1643-2.29970.273730.1734281549
2.2997-2.47690.23871460.1612571999
2.4769-2.72540.21771470.1733573898
2.7254-3.11830.25111470.1813571898
3.1183-3.92280.22691280.1982499285
3.9228-18.80590.32531320.26515386

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