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- PDB-2bpu: The Kedge Holmium Derivative of Hen Egg-White Lysozyme at high re... -

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Basic information

Entry
Database: PDB / ID: 2bpu
TitleThe Kedge Holmium Derivative of Hen Egg-White Lysozyme at high resolution from Single Wavelength Anomalous Diffraction
ComponentsLYSOZYME C
KeywordsHYDROLASE / HOLMIUM / KEDGE / ULTRA HIGH ENERGY / HIGH RESOLUTION / COMPTON / EXPERIMENTAL PHASES / ALLERGEN / HYDROLASE BACTERIOLYTIC ENZYME / GLYCOSIDASE / SAD
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
HOLMIUM ATOM / Lysozyme C
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsJakoncic, J. / Di Michiel, M. / Zhong, Z. / Honkimaki, V. / Jouanneau, Y. / Stojanoff, V.
CitationJournal: J.Appl.Crystallogr. / Year: 2006
Title: Anomalous Diffraction at Ultra-High Energy for Protein Crystallography.
Authors: Jakoncic, J. / Di Michiel, M. / Zhong, Z. / Honkimaki, V. / Jouanneau, Y. / Stojanoff, V.
History
DepositionApr 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_database_status.status_code_sf / _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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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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)14,9558
Polymers14,3311
Non-polymers6247
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.707, 78.707, 37.325
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-1134-

HO

21A-2041-

HOH

31A-2061-

HOH

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Components

#1: Protein LYSOZYME C / LYSOZYME HEWL / 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) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-HO / HOLMIUM ATOM


Mass: 164.930 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ho
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 39.01 %
Crystal growpH: 4.5 / Details: pH 4.50

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.2229
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.2229 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 49334 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.9
Reflection shellResolution: 1.35→1.4 Å / Mean I/σ(I) obs: 2.2 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→27.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.927 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.06
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED LOOPS WERE MANUALLY CONSTRUCTED. 124 (TOTAL RESIDUES 129) WERE AUTOMATICALLY CONSTRUCTED WITH ARP.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1338 5.1 %RANDOM
Rwork0.183 ---
obs0.184 25072 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.35→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 111 1119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211038
X-RAY DIFFRACTIONr_bond_other_d0.0020.02898
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9041409
X-RAY DIFFRACTIONr_angle_other_deg0.86632082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3523.13751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.82615171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4331511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02231
X-RAY DIFFRACTIONr_nbd_refined0.2380.2239
X-RAY DIFFRACTIONr_nbd_other0.1840.2914
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2532
X-RAY DIFFRACTIONr_nbtor_other0.0820.2572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.061.5641
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64121020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3593426
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.64.5387
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.38 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 93
Rwork0.241 1723

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