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- PDB-4tws: Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.4... -

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Basic information

Entry
Database: PDB / ID: 4tws
TitleGadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.45 A Resolution
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / Gadolinium
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DO3 / GADOLINIUM ATOM / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHolton, J.M. / Classen, S. / Frankel, K.A. / Tainer, J.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM105404 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50-GM073210 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50-GM082250 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM094625 United States
CitationJournal: Febs J. / Year: 2014
Title: The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures.
Authors: Holton, J.M. / Classen, S. / Frankel, K.A. / Tainer, J.A.
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Aug 3, 2016Group: Derived calculations / Structure summary
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: 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 / diffrn_radiation_wavelength / 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 / _diffrn_radiation_wavelength.wavelength / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,59225
Polymers14,3311
Non-polymers2,26124
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-176 kcal/mol
Surface area6770 Å2
Unit cell
Length a, b, c (Å)77.220, 77.220, 38.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 297 molecules

#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-DO3 / 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID


Mass: 404.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H32N4O7
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Tetragonal crystals were grown by the vapour-diffusion technique using the hanging-drop method, with 0.7-1.0 M sodium chloride and 50 mM sodium acetate buffer at pH 4.5. Derivative crystals ...Details: Tetragonal crystals were grown by the vapour-diffusion technique using the hanging-drop method, with 0.7-1.0 M sodium chloride and 50 mM sodium acetate buffer at pH 4.5. Derivative crystals containing gadolinium were obtained using concentrations of Gd-HPDO3A in the range 10-100 mM.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.97934
SYNCHROTRONALS 12.3.120.97934
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 26, 2007
ADSC QUANTUM 3152CCDJun 25, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
21
ReflectionResolution: 1.45→38.61 Å / Num. obs: 19784 / % possible obs: 87.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 11.64 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.57
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 1.86 / % possible all: 39

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H87

1h87


Resolution: 1.45→38.61 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / Phase error: 15.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.161 975 4.93 %
Rwork0.138 --
obs0.139 19783 92.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.7 Å2
Refinement stepCycle: LAST / Resolution: 1.45→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 105 273 1379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061293
X-RAY DIFFRACTIONf_angle_d1.4241876
X-RAY DIFFRACTIONf_dihedral_angle_d22.416528
X-RAY DIFFRACTIONf_chiral_restr0.065166
X-RAY DIFFRACTIONf_plane_restr0.004222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4505-1.52690.231950.22081719X-RAY DIFFRACTION61
1.5269-1.62260.23231360.16942478X-RAY DIFFRACTION87
1.6226-1.74790.18871470.15382831X-RAY DIFFRACTION99
1.7479-1.92380.15771590.13962868X-RAY DIFFRACTION100
1.9238-2.20210.1381410.12842888X-RAY DIFFRACTION100
2.2021-2.77430.16161610.13112925X-RAY DIFFRACTION100
2.7743-38.62370.14311360.12863099X-RAY DIFFRACTION100

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