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- PDB-1hf4: STRUCTURAL EFFECTS OF MONOVALENT ANIONS ON POLYMORPHIC LYSOZYME C... -

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Basic information

Entry
Database: PDB / ID: 1hf4
TitleSTRUCTURAL EFFECTS OF MONOVALENT ANIONS ON POLYMORPHIC LYSOZYME CRYSTALS
ComponentsLYSOZYME
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL)
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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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: 2000
Title: Novel Approach to Phasing Proteins: Derivatization by Short Cryo-Soaking with Halides
Authors: Dauter, Z. / Dauter, M. / Rajashankar, K.R.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Anomalous Signal of Solvent Bromides Used for Phasing of Lysozyme
Authors: Dauter, Z. / Dauter, M.
#3: 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.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structures of Monoclinic Lysozyme Iodide at 1.6 A and of Triclinic Lysozyme Nitrate at 1.1 A.
Authors: Steinrauf, L.K.
#5: 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.
#6: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: High-Resolution Structure (1.33 A) of a Hew Lysozyme Tetragonal Crystal Grown in the Apcf Apparatus. Data and Structural Comparison with a Crystal Grown Under Microgravity from Spacehab-01 Mission.
Authors: Vaney, M.C. / Maignan, S. / Ries-Kautt, M. / Ducruix, A.
History
DepositionNov 29, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 7, 2001Provider: 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,20412
Polymers28,6622
Non-polymers54210
Water4,522251
1
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5405
Polymers14,3311
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6647
Polymers14,3311
Non-polymers3336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)27.940, 62.730, 60.250
Angle α, β, γ (deg.)90.00, 90.76, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 1.63 Å3/Da / Density % sol: 24 %
Crystal growTemperature: 293 K / pH: 4.5
Details: CRYSTALS OF NITRATE-LYSOZYME WERE GROWN UNDER A MICRO GRAVITY ENVIRONMENT DURING THE USML-2 MISSION LAUNCHED ON OCTOBER 1995 (SHUTTLE COLUMBIA). THE CRYSTALLIZATION SETUP WAS THE APCF ...Details: CRYSTALS OF NITRATE-LYSOZYME WERE GROWN UNDER A MICRO GRAVITY ENVIRONMENT DURING THE USML-2 MISSION LAUNCHED ON OCTOBER 1995 (SHUTTLE COLUMBIA). THE CRYSTALLIZATION SETUP WAS THE APCF DEVELOPPED BY EUROPEAN SPACE AGENCY. PROTEIN CONCENTRATION 10 MG/ML IN 50 MM SODIUM ACETATE BUFFER AT PH 4.5. GRADIENT CONCENTRATION APPLIED FROM 0 TO FINAL 290 MM AT 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
250 mMsodium acetate11
30-290 mMsodium nitrate12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→10 Å / Num. obs: 35206 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.1
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.5 / % possible all: 87
Reflection
*PLUS
Rmerge(I) obs: 0.123

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Processing

Software
NameVersionClassification
X-PLOR3.853refinement
MOSFLMdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
X-PLOR3.853phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LYM

5lym


Resolution: 1.45→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE LOOP ARG73-ASN74 OF CHAIN B WAS MODELED WITH ALTERNATE POSITIONS. IN CONTACT WITH THESE TWO LOOPS CONFORMATIONS, TWO SODIUM IONS NA+ WERE REFINED WITH ALTERNATE POSITIONS. ATOM ...Details: THE LOOP ARG73-ASN74 OF CHAIN B WAS MODELED WITH ALTERNATE POSITIONS. IN CONTACT WITH THESE TWO LOOPS CONFORMATIONS, TWO SODIUM IONS NA+ WERE REFINED WITH ALTERNATE POSITIONS. ATOM OCCUPANCIES WERE REFINED FOR NA+ 350 AND SOME NITRATE IONS: NO3-807 AND NO3-808, BUT NO ALTERNATE POSITIONS WERE MODELLED. ALTHOUGH THERE ARE SOME BUMPS BETWEEN ATOMS OF THE STRUCTURE, THESE ATOMS ARE CLEARLY DEFINED INTO THE ELECTRON DENSITIES.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3499 10 %RANDOM
Rwork0.215 ---
obs0.215 31225 95.5 %-
Displacement parametersBiso mean: 16.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.45→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 34 251 2287
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.14
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: 1.45→1.52 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.39 403 11.3 %
Rwork0.34 3549 -
obs--87 %
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: 3.853 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.14

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