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- PDB-2vb1: HEWL at 0.65 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 2vb1
TitleHEWL at 0.65 angstrom resolution
ComponentsLYSOZYME C
KeywordsHYDROLASE / ANTIMICROBIAL / TRICLINIC HEWL / ATOMIC RESOLUTION / LYSOZYME / ALLERGEN / GLYCOSIDASE / BACTERIOLYTIC ENZYME
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
ACETATE ION / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.65 Å
AuthorsWang, J. / Dauter, M. / Alkire, R. / Joachimiak, A. / Dauter, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Triclinic Lysozyme at 0.65 A Resolution.
Authors: Wang, J. / Dauter, M. / Alkire, R. / Joachimiak, A. / Dauter, Z.
History
DepositionSep 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Mar 8, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,13414
Polymers14,3311
Non-polymers80313
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)27.070, 31.250, 33.760
Angle α, β, γ (deg.)87.98, 108.00, 112.11
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.: 1 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / Cell: EGG / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.69 Å3/Da / Density % sol: 26.9 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.7
Details: SITTING DROP METHOD. PROTEIN SOLUTION: 35 MG/ML HEWL, 0.02 M NA ACETATE BUFFER PH 4.7 WELL SOLUTION: 1 M NANO3, 0.1 M NA ACETATE BUFFER PH 4.7, 20 % ETHYLENE GLYCOL PROTEIN AND WELL ...Details: SITTING DROP METHOD. PROTEIN SOLUTION: 35 MG/ML HEWL, 0.02 M NA ACETATE BUFFER PH 4.7 WELL SOLUTION: 1 M NANO3, 0.1 M NA ACETATE BUFFER PH 4.7, 20 % ETHYLENE GLYCOL PROTEIN AND WELL SOLUTIONS MIXED 1:1 IN A DROP AND SEEDED

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.65
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 5, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 0.65→30 Å / Num. obs: 187165 / % possible obs: 97.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 36.2
Reflection shellResolution: 0.65→0.67 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.2 / % possible all: 67.3

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
ACORNphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 0.65→30 Å / Num. parameters: 14111 / Num. restraintsaints: 20151 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.0952 9365 5 %RANDOM
all0.0839 187165 --
obs0.0848 -97.5 %-
Refine analyzeNum. disordered residues: 65 / Occupancy sum hydrogen: 976.69 / Occupancy sum non hydrogen: 1172.99
Refinement stepCycle: LAST / Resolution: 0.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 52 170 1223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.024
X-RAY DIFFRACTIONs_angle_d0.06
X-RAY DIFFRACTIONs_similar_dist0.04
X-RAY DIFFRACTIONs_from_restr_planes0.0355
X-RAY DIFFRACTIONs_zero_chiral_vol0.12
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.141
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.098
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.085

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