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- PDB-1b2k: Structural effects of monovalent anions on polymorphic lysozyme c... -

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Basic information

Entry
Database: PDB / ID: 1b2k
TitleStructural effects of monovalent anions on polymorphic lysozyme crystals
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL)
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
IODIDE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVaney, M.C. / Broutin, I. / Ries-Kautt, M. / Ducruix, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structural effects of monovalent anions on polymorphic lysozyme crystals.
Authors: Vaney, M.C. / Broutin, I. / Retailleau, P. / Douangamath, A. / Lafont, S. / Hamiaux, C. / Prange, T. / Ducruix, A. / Ries-Kautt, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Refinement of Triclinic Hen Egg-White Lysozyme at Atomic Resolution
Authors: Walsh, M.A. / Schneider, T.R. / Sieker, L.C. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structures of Monoclinic Lysozyme Iodide at 1.6 Ang. And of Triclinic Lysozyme Nitrate at 1.1 Ang
Authors: Steinrauf, L.K.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Locations of Bromide Ions in Tetragonal Lysozyme Crystals
Authors: Lim, K. / Nadarajah, A. / Forsythe, E.L. / Pusey, M.L.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: High-Resolution Structure (1.33 Ang.) Of a Hewl Lysozyme Tetragonal Crystal Grown in the Apcf Apparatus. Data and Structural Comparison with a Crystal Grown Under Microgravity from Spachab-01 Mission
Authors: Vaney, M.C. / Maignan, S. / Ries-Kautt, M. / Ducruix, A.
History
DepositionNov 26, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
B: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,82019
Polymers28,6622
Non-polymers2,15717
Water5,242291
1
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,60011
Polymers14,3311
Non-polymers1,26910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2198
Polymers14,3311
Non-polymers8887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.730, 62.790, 59.840
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (LYSOZYME) / HEN (GALLUS GALLUS) EGG-WHITE LYSOZYME / MUCOPEPTIDE / N-ACETYLMURAMYL HYDROLASE


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: CYTOPLASM (WHITE) / Tissue: EGG WHITE / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsWATER MOLECULE HOH 746, WELL-DEFINED IN THE DENSITY, IS HYDROGEN-BONDED WITH NE OF ARG 112A WITH A ...WATER MOLECULE HOH 746, WELL-DEFINED IN THE DENSITY, IS HYDROGEN-BONDED WITH NE OF ARG 112A WITH A DISTANCE OF 3.45 ANG.

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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: 1.8 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 291 K / pH: 4.5
Details: THE ISOIONIC PROTEIN HEWL WAS ACIDIFIED BY ADDING OF HI UNTIL THE PH 4.5 WAS REACHED AT 291K WERE 25 MG/ML OF PROTEIN AND 0.07 M OF NAI VERSUS A WELL CONTAINING 0.14 M OF NAI AT PH4.5
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Details: pH is adjusted to 4.5 with HI, drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mg/mlprotein1drop
20.14 M1reservoirNaI

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 1.6→13.3 Å / Num. obs: 26152 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.095 / Net I/σ(I): 5.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.54 / % possible all: 95.6
Reflection
*PLUS
Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 95.6 % / Rmerge(I) obs: 0.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Agrovatadata reduction
CCP4data reduction
AMoREphasing
X-PLOR3.851refinement
Agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.6→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2612 10 %RANDOM
Rwork0.198 ---
obs0.198 26000 96.6 %-
Displacement parametersBiso mean: 16.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 19 291 2324
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.16
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.51.5
X-RAY DIFFRACTIONx_mcangle_it2.732
X-RAY DIFFRACTIONx_scbond_it3.212
X-RAY DIFFRACTIONx_scangle_it3.72.5
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.345 320 9.58 %
Rwork0.294 2861 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.17
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6

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