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- PDB-1iee: STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME AT 0.94 A FROM CRY... -

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Basic information

Entry
Database: PDB / ID: 1iee
TitleSTRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME AT 0.94 A FROM CRYSTALS GROWN BY THE COUNTER-DIFFUSION METHOD
ComponentsLYSOZYME C
KeywordsHYDROLASE / LYSOZYME / 1 / 4-BETA-N-ACETYLMURAMIDASE C
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å
AuthorsSauter, C. / Otalora, F. / Gavira, J.-A. / Vidal, O. / Giege, R. / Garcia-Ruiz, J.-M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of tetragonal hen egg-white lysozyme at 0.94 A from crystals grown by the counter-diffusion method.
Authors: Sauter, C. / Otalora, F. / Gavira, J.A. / Vidal, O. / Giege, R. / Garcia-Ruiz, J.M.
#1: Journal: To be Published
Title: A SUPERSATURATION WAVE OF PROTEIN CRYSTALLIZATION
Authors: Garcia-Ruiz, J.-M. / Otalora, F. / Novella, M.-L. / Gavira, J.-A. / Sauter, C. / Vidal, O.
History
DepositionApr 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Aug 9, 2023Group: 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 / struct_site
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_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_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_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,5317
Polymers14,3311
Non-polymers2006
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.061, 77.061, 37.223
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-1092-

HOH

21A-1103-

HOH

31A-1139-

HOH

41A-1169-

HOH

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Components

#1: Protein LYSOZYME C / 1 / 4-BETA-N-ACETYLMURAMIDASE C


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: EGG WHITE / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.67 Å3/Da / Density % sol: 26.7 %
Crystal growTemperature: 293 K / Method: counter-diffusion in modified APCF reactors / pH: 4.5
Details: CRYSTALLISATION TOOK PLACE IN THE EUROPEAN SPACE AGENCY (ESA) ADVANCED PROTEIN CRYSTALLISATION FACILITY (APCF) ONBOARD THE NASA SPACE SHUTTLE'S STS-95 MISSION. A NEW APCF REACTOR WITH A LONG ...Details: CRYSTALLISATION TOOK PLACE IN THE EUROPEAN SPACE AGENCY (ESA) ADVANCED PROTEIN CRYSTALLISATION FACILITY (APCF) ONBOARD THE NASA SPACE SHUTTLE'S STS-95 MISSION. A NEW APCF REACTOR WITH A LONG PROTEIN CHAMBER (67 MM) WAS DESIGNED TO PERFORM CRYSTALLIZATION USING THE COUNTER-DIFFUSION METHOD UNDER MICROGRAVITY CONDITIONS. THE PROTEIN CHAMBER WAS FILLED WITH A SOLUTION OF 99 MG/ML OF HEN EGG WHITE LYSOZYME (SUPPLIED BY SEIKAGAKU, BATCH NUMBER 100940, LOT E96302) DISSOLVED IN 0.05 M ACETATE BUFFER (PH 4.5). THE SALT CHAMBER CONTAINED 20% W/V NACL AND 0.05 M ACETATE BUFFER (PH 4.5). THE ROTATORY PLUG CONNECTING THE PROTEIN AND THE SALT CHAMBERS WAS FILLED WITH 10% W/V NACL, 0.5% W/V AGAROSE GEL AND 0.05 M ACETATE BUFFER. CRYSTALLISATION TOOK PLACE IN MICROGRAVITY AT 20+/-0.1 C., Counter-Diffusion in modified APCF reactors, temperature 293K
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7B10.8337
SYNCHROTRONEMBL/DESY, HAMBURG X1120.9057
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEDec 10, 1998
MARRESEARCH2IMAGE PLATEDec 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.83371
20.90571
ReflectionResolution: 0.94→31 Å / Num. all: 402070 / Num. obs: 72390 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.5
Reflection shellResolution: 0.94→0.96 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3912 / % possible all: 88.6
Reflection
*PLUS
Num. measured all: 402070
Reflection shell
*PLUS
% possible obs: 88.6 %

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LSA

1lsa


Resolution: 0.94→31 Å / Num. parameters: 13632 / Num. restraintsaints: 19082 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: WATER OCCUPANCIES REFINED. SIX SECTIONS OF THE MAIN CHAIN MODELED IN TWO DISCRETE CONFORMATIONS (17-19,58-62,68-75,77-78,86-88,108-110).
RfactorNum. reflection% reflectionSelection details
Rfree0.1509 3655 -RANDOM
Rwork0.1233 ---
all0.1226 72390 --
obs0.1226 72390 98.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Displacement parametersBiso mean: 14.4 Å2
Refine analyzeNum. disordered residues: 37 / Occupancy sum hydrogen: 956.3 / Occupancy sum non hydrogen: 1173.6
Refinement stepCycle: LAST / Resolution: 0.94→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 6 255 1490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.115
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.067
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.072
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
0.94-0.960.3X-RAY DIFFRACTION391288.6
0.96-0.970.222X-RAY DIFFRACTION2052100
0.97-0.990.184X-RAY DIFFRACTION3918100
0.99-1.010.167X-RAY DIFFRACTION359499.9
1.01-1.030.15X-RAY DIFFRACTION3332100
1.03-310.118X-RAY DIFFRACTION5558299.5
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 31 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.123
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.031
X-RAY DIFFRACTIONs_chiral_restr0.11

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