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- PDB-1v7t: Triclinic lysozyme with low solvent content obtained by phase tra... -

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Basic information

Entry
Database: PDB / ID: 1v7t
TitleTriclinic lysozyme with low solvent content obtained by phase transition
ComponentsLysozyme C
KeywordsHYDROLASE / Transformed crystal / phase transition
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsHarata, K. / Akiba, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Phase transition of triclinic hen egg-white lysozyme crystal associated with sodium binding.
Authors: Harata, K. / Akiba, T.
History
DepositionDec 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_label_seq_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,0189
Polymers28,6622
Non-polymers3567
Water4,017223
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6026
Polymers14,3311
Non-polymers2715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4163
Polymers14,3311
Non-polymers852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.930, 39.970, 42.390
Angle α, β, γ (deg.)88.00, 95.44, 90.58
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.51 Å3/Da / Density % sol: 18.5 %
Crystal growTemperature: 313 K / pH: 4.5
Details: sodium nitrate, sodium acetate, pH 4.5, phase transition, temperature 313K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Apr 11, 2002 / Details: Confocal Max-Flux
RadiationMonochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.13→39.94 Å / Num. all: 64571 / Num. obs: 52044 / % possible obs: 80.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.18 % / Rmerge(I) obs: 0.034
Reflection shellResolution: 1.13→1.17 Å / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 3.65 / % possible all: 46.4

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Processing

Software
NameVersionClassification
SaintPlusdata reduction
X-PLORmodel building
SHELXL-97refinement
SMARTV. 6000data reduction
SAINTPLUSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→39.94 Å / Num. parameters: 20892 / Num. restraintsaints: 26460 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.162 2601 -random
Rwork0.114 ---
all0.119 52044 --
obs0.119 52044 80.6 %-
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 1917 / Occupancy sum non hydrogen: 2206.9
Refinement stepCycle: LAST / Resolution: 1.13→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 22 223 2247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_from_restr_planes0.404
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.057
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.057
X-RAY DIFFRACTIONs_approx_iso_adps0.084
LS refinement shellResolution: 1.13→1.21 Å /
RfactorNum. reflection
Rwork0.165 -
obs-5049

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