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- PDB-1h87: Gadolinium derivative of tetragonal Hen Egg-White Lysozyme at 1.7... -

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Basic information

Entry
Database: PDB / ID: 1h87
TitleGadolinium derivative of tetragonal Hen Egg-White Lysozyme at 1.7 A resolution
ComponentsLYSOZYME C
KeywordsHYDROLASE / GADOLINIUM DERIVATIVE / LYSOZYME / O-GLYCOSYL HYDROLASE
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
Chem-DO3 / GADOLINIUM ATOM / Lysozyme C
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGirard, E. / Chantalat, L. / Vicat, J. / Kahn, R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Gd-Hp-Do3A, a Complex to Obtain High-Phasing-Power Heavy Atom Derivatives for Sad and MAD Experiments. Results with Tetragonal Hen Egg-White Lysozyme
Authors: Girard, E. / Chantalat, L. / Vicat, J. / Kahn, R.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Thermal Expansion of Hen-Egg-White Lysozyme. Comparison of the 1.9 Angstroms Resolution Structures of the Tetragonal Form of the Enzyme at 100K and 298K
Authors: Young, A.C.M. / Tilton, R.F. / Dewan, J.C.
#2: Journal: J.Synchrotron Radia. / Year: 2001
Title: High-Pressure Protein Crystallography (Hppx): Instrumentation, Methodology and Results on Lysozyme Crystals
Authors: Fourme, R. / Kahn, R. / Mezouar, M. / Girard, E. / Hoerentrup, C. / Prange, T. / Ascone, I.
History
DepositionJan 25, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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.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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5969
Polymers14,3311
Non-polymers1,2658
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.250, 77.250, 38.660
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-2058-

HOH

21A-2062-

HOH

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Components

#1: Protein LYSOZYME C


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PURCHASED FROM BOEHRINGER MANNHEIM BATCH NUMBER 13032022-90
Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-DO3 / 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID


Mass: 404.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32N4O7
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.02 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 293 K / pH: 4.5
Details: NACL 0.8 M, SODIUM ACETATE 50 MM, PH4.5, GD-HP-DO3A 100MM, [PROT]=40 MG/ML, 293 K, pH 4.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.7-1.0 M1reservoirNaCl
250 mMsodium acetate1reservoirpH4.5
3100 mMprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→17.2 Å / Num. obs: 12876 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 12.5 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.059 / Net I/σ(I): 8.1
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4 / Rsym value: 0.173 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 166568 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 96.8 % / Rmerge(I) obs: 0.173

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 6LYT

6lyt


Resolution: 1.72→27.33 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1120223.55 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SOME OF THE SIDE CHAIN ATOMS OF RESIDUES ARG21, ARG45, ARG61 AND ARG73 HAVE A POORLY DEFINED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2169 9.3 %RANDOM
Rwork0.18 ---
obs0.18 23249 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6549 Å2 / ksol: 0.336137 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2---1.31 Å20 Å2
3---2.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.72→27.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 62 154 1217
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.171.5
X-RAY DIFFRACTIONc_mcangle_it0.32
X-RAY DIFFRACTIONc_scbond_it0.876
X-RAY DIFFRACTIONc_scangle_it1.237.5
LS refinement shellResolution: 1.72→1.83 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 302 8.6 %
Rwork0.25 3192 -
obs--89.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MY_CNS_ION.PARAMMY_CNS_ION.TOP
X-RAY DIFFRACTION4GD_HP-DO3A.PARAMGD_HP-DO3A.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rwork: 0.25

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