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- PDB-6gnl: Zr(IV)-substituted Keggin directly binding to the side chain of H... -

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Basic information

Entry
Database: PDB / ID: 6gnl
TitleZr(IV)-substituted Keggin directly binding to the side chain of Hen Egg-White Lysozyme (HEWL)
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / co-crystal / hydrolysis / catalysis
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
ZIRCONIUM(IV) PHOSPHOTUNGSTATE KEGGIN / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.23 Å
AuthorsVandebroek, L. / Van Meervelt, L. / Parac-Vogt, T.N.
CitationJournal: Acta Crystallogr C Struct Chem / Year: 2018
Title: Direct observation of the ZrIVinteraction with the carboxamide bond in a noncovalent complex between Hen Egg White Lysozyme and a Zr-substituted Keggin polyoxometalate.
Authors: Vandebroek, L. / Van Meervelt, L. / Parac-Vogt, T.N.
History
DepositionMay 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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 / 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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_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)19,9766
Polymers14,3311
Non-polymers5,6455
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.701, 77.701, 37.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

21A-418-

HOH

31A-422-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen 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-ZKG / ZIRCONIUM(IV) PHOSPHOTUNGSTATE KEGGIN


Mass: 2769.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O39PW11Zr / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.99 Å3/Da / Density % sol: 38.32 % / Mosaicity: 0.1 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 7
Details: 1.75 mM HEWL, 0.88 mM 2:2 Zr(IV)-Keggin, 1.5 M NH4Cl, 0.1 M Bis-Tris propane pH = 7.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA11
SYNCHROTRONSLS X06DA21.21
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.211
ReflectionResolution: 1.23→38.85 Å / Num. obs: 34264 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 13.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.015 / Rrim(I) all: 0.042 / Net I/σ(I): 32.4 / Num. measured all: 240940
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.23-1.257.10.5511220017250.8930.2220.5953.5100
6.62-38.855.80.0316042770.9990.0120.032104.599

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.66 Å38.85 Å
Translation4.66 Å38.85 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
Aimless0.5.32data scaling
PHASER2.8.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1LYZ

1lyz


Resolution: 1.23→38.85 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.21 / Stereochemistry target values: ML / Details: Phenix.refine v 1.12
RfactorNum. reflection% reflection
Rfree0.1713 3260 5.08 %
Rwork0.1475 60928 -
obs0.1487 64188 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.7 Å2 / Biso mean: 19.0469 Å2 / Biso min: 7.61 Å2
Refinement stepCycle: final / Resolution: 1.23→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 159 168 1328
Biso mean--25.07 28.73 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151302
X-RAY DIFFRACTIONf_angle_d1.2662136
X-RAY DIFFRACTIONf_chiral_restr0.089163
X-RAY DIFFRACTIONf_plane_restr0.006196
X-RAY DIFFRACTIONf_dihedral_angle_d12.361591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.23-1.24840.25851540.22826372791100
1.2484-1.26790.25361330.21126322765100
1.2679-1.28870.20831520.189126842836100
1.2887-1.31090.22921670.18526152782100
1.3109-1.33470.17671440.171926432787100
1.3347-1.36040.18612000.162526022802100
1.3604-1.38820.19291440.161626512795100
1.3882-1.41840.21031440.154926452789100
1.4184-1.45140.16481570.150126412798100
1.4514-1.48770.18051340.141926512785100
1.4877-1.52790.21671310.14126632794100
1.5279-1.57280.18591480.144626632811100
1.5728-1.62360.21441160.134126442760100
1.6236-1.68160.14941260.129226632789100
1.6816-1.7490.1741360.128826722808100
1.749-1.82860.16591430.13326572800100
1.8286-1.9250.17151290.124526452774100
1.925-2.04560.15871200.131126942814100
2.0456-2.20350.12191160.123726532769100
2.2035-2.42520.1411160.13312675279199
2.4252-2.77610.16741350.14022632276799
2.7761-3.49720.16561700.149926172787100
3.4972-38.86990.17621450.171426492794100

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