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- PDB-5lyz: Real-space refinement of the structure of hen egg-white lysozyme -

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Entry
Database: PDB / ID: 5lyz
TitleReal-space refinement of the structure of hen egg-white lysozyme
ComponentsHEN EGG WHITE LYSOZYME
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDiamond, R. / Phillips, D.C. / Blake, C.C.F. / North, A.C.T.
Citation
Journal: J.Mol.Biol. / Year: 1974
Title: Real-space refinement of the structure of hen egg-white lysozyme.
Authors: Diamond, R.
#1: Journal: Lysozyme / Year: 1974
Title: Crystallographic Studies of Lysozyme and its Interactions with Inhibitors and Substrates
Authors: Phillips, D.C.
#2: Journal: The Enzymes,Third Edition / Year: 1972
Title: Vertebrate Lysozymes
Authors: Imoto, T. / Johnson, L.N. / North, A.C.T. / Phillips, D.C. / Rupley, J.A.
#3: Journal: J.Mol.Biol. / Year: 1975
Title: An X-Ray Study of the Structure and Binding Properties of Iodine-Inactivated Lysozyme
Authors: Beddell, C.R. / Blake, C.C.F. / Oatley, S.J.
#4: Journal: J.Mol.Biol. / Year: 1974
Title: Energy Refinement of Hen Egg-White Lysozyme
Authors: Levitt, M.
#5: Journal: Proc.R.Soc.London,Ser.B / Year: 1967
Title: On the Conformation of the Hen Egg-White Lysozyme Molecule
Authors: Blake, C.C.F. / Mair, G.A. / North, A.C.T. / Phillips, D.C. / Sarma, V.R.
#6: Journal: Proc.R.Soc.London,Ser.B / Year: 1967
Title: Crystallographic Studies of the Activity of Hen Egg-White Lysozyme
Authors: Blake, C.C.F. / Johnson, L.N. / Mair, G.A. / North, A.C.T. / Phillips, D.C. / Sarma, V.R.
#7: Journal: Sci.Am. / Year: 1966
Title: The Three-Dimensional Structure of an Enzyme Molecule
Authors: Phillips, D.C.
#8: Journal: Nature / Year: 1965
Title: Structure of Hen Egg-White Lysozyme, a Three-Dimensional Fourier Synthesis at 2 Angstroms Resolution
Authors: Blake, C.C.F. / Koenig, D.F. / Mair, G.A. / North, A.C.T. / Phillips, D.C. / Sarma, V.R.
#9: Journal: Nature / Year: 1965
Title: Structure of Some Crystalline Lysozyme-Inhibitor Complexes Determined by X-Ray Analysis at 6 Angstroms Resolution
Authors: Johnson, L.N. / Phillips, D.C.
#10: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#11: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionFeb 1, 1975Processing site: BNL
Revision 1.0Apr 12, 1977Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.100, 79.100, 37.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: POSSIBLE HYDROGEN BONDS TO CARBONYL OF TYR 53, N OF LEU 56, OG OF SER 91
2: POSSIBLE HYDROGEN BONDS TO HOH 44, HOH 61, CARBONYL OF ASP 87, N AND OG OF SER 91
3: POSSIBLE HYDROGEN BONDS TO HOH 4, NZ OF LYS 1, CARBONYL OF VAL 2, OE1 OF GLU 7
4: POSSIBLE HYDROGEN BONDS TO HOH 3, HOH 40, OE OF GLU 7 POSSIBLE HYDROGEN BOND TO NE OF ARG 5
5: POSSIBLE HYDROGEN BONDS TO NE OF ARG 14, CARBONYL OF ARG 128, HOH 40
6: POSSIBLE HYDROGEN BONDS TO NZ OF LYS 33, NE OF ARG 73, HOH 40
7: POSSIBLE HYDROGEN BONDS TO CARBONYLS OF ILE 124, CYS 127, HOH 39
8: POSSIBLE HYDROGEN BONDS TO OD1 OF ASP 48, N OF GLY 126 / 9: POSSIBLE HYDROGEN BOND TO NE OF ARG 61 / 10: POSSIBLE HYDROGEN BOND TO NE OF ARG 5 / 11: POSSIBLE HYDROGEN BOND TO N OF CYS 6 / 12: POSSIBLE HYDROGEN BOND TO NE OF ARG 14 / 13: POSSIBLE HYDROGEN BOND TO OG OF SER 24 / 14: POSSIBLE HYDROGEN BOND TO AMIDE OF GLN 121 / 15: POSSIBLE HYDROGEN BONDS TO HOH 24A, AMIDE OF GLN 121 / 16: POSSIBLE HYDROGEN BOND TO OD OF ASP 119 / 17: POSSIBLE HYDROGEN BOND TO HOH 35, NEAR NE1 OF TRP 123
18: POSSIBLE HYDROGEN BONDS TO N OF TYR 23, ND2 OF ASN 27, NE OF ARG 114
19: POSSIBLE HYDROGEN BOND TO ND2 OF ASN 37
20: POSSIBLE HYDROGEN BOND TO CARBONYL OF GLY 67, AND NEAR VAL 2
21: POSSIBLE HYDROGEN BONDS TO N OF LYS 1, OG OF SER 86, HOH 34 PRO 79G
22: POSSIBLE HYDROGEN BONDS TO N OF LYS 1, OD1 OF ASN 39, OE1 OF GLN 41, HOH 22 COG 66
23: POSSIBLE HYDROGEN BOND TO HOH 21 OD 65G / 24: POSSIBLE HYDROGEN BONDS TO OG OF SER 24, N OF GLY 26
25: POSSIBLE HYDROGEN BONDS TO CARBONYL OF THR 118, N OF VAL 120, HOH 24A
26: POSSIBLE HYDROGEN BONDS TO HOH 14, HOH 24 / 27: POSSIBLE HYDROGEN BONDS TO HOH 26, NE OF ARG 114
28: POSSIBLE HYDROGEN BONDS TO CARBONYL OF ARG 114, HOH 25, HOH 35
29: POSSIBLE HYDROGEN BONDS TO HOH 28, CARBONYL OF PHE 34 COE 22
30: POSSIBLE HYDROGEN BONDS TO HOH 27, HOH 29 NODE 19
31: POSSIBLE HYDROGEN BONDS TO CARBONYL OF GLU 35, HOH 28, HOH 30, HOH 31
32: POSSIBLE HYDROGEN BONDS TO HOH 29, HOH 32 NEH G68
33: POSSIBLE HYDROGEN BONDS TO ND2 OF ASN 44, OE1 OF GLN 57, HOH 29
34: POSSIBLE HYDROGEN BONDS TO CARBONYL OF SER 36, ND2 OF ASN 39, HOH 30, HOH 33 G68
35: POSSIBLE HYDROGEN BONDS TO ND2 OF ASN 37, HOH 32 G67 / 36: POSSIBLE HYDROGEN BOND TO HOH 20, NEAR OG OF SER 26 / 37: POSSIBLE HYDROGEN BONDS TO HOH 16, HOH 26, HOH 55 E116
38: POSSIBLE HYDROGEN BONDS TO CARBONYL OF PHE 34, NH1 OF ARG 114 E22
39: POSSIBLE HYDROGEN BONDS TO CARBONYL OF GLN 41, NE OF ARG 68 OEHG53
40: POSSIBLE HYDROGEN BONDS TO OG1 OF THR 40, CARBONYL OF LEU 84, OG OF SER 86 N86
41: POSSIBLE HYDROGEN BONDS TO HOH 7, HOH 40, NE OF ARG 14
42: POSSIBLE HYDROGEN BONDS TO HOH 4, HOH 5, HOH 6, HOH 39, HOH 41, ND1 OF HIS 15
43: POSSIBLE HYDROGEN BONDS TO HOH 40, NE OF ARG 14, OD2 OF ASP 87
44: POSSIBLE HYDROGEN BONDS TO CARBONYL OF LYS 13, N OF ASP 18, HOH 63
45: POSSIBLE HYDROGEN BONDS TO CARBONYLS OF LEU 83, SER 85
46: POSSIBLE HYDROGEN BONDS TO N OF ALA 110, ND2 OF ASN 113, HOH 47 HOH 32
47: POSSIBLE HYDROGEN BOND TO OD1 OF ASN 113 / 48: POSSIBLE HYDROGEN BONDS TO HOH 45, HOH 48
49: POSSIBLE HYDROGEN BONDS TO HOH 47, OE1 OF GLU 35, HOH 58, HOH 59
50: POSSIBLE HYDROGEN BONDS TO N OF GLU 7, N OF THR 118 / 51: POSSIBLE HYDROGEN BONDS TO OG OF SER 85, HOH 51, HOH 66 / 52: POSSIBLE HYDROGEN BOND TO HOH 50 / 53: POSSIBLE HYDROGEN BOND TO HOH 53 / 54: POSSIBLE HYDROGEN BOND TO HOH 52 / 55: POSSIBLE HYDROGEN BOND TO HOH 35 / 56: POSSIBLE HYDROGEN BOND TO NE OF ARG 14
57: POSSIBLE HYDROGEN BONDS TO HOH 57A, CARBONYLS OF ARG 14, HIS 15
58: POSSIBLE HYDROGEN BOND TO HOH 57 / 59: POSSIBLE HYDROGEN BONDS TO HOH 48, OD2 OF ASP 52 / 60: POSSIBLE HYDROGEN BONDS TO HOH 48, HOH 60 / 61: POSSIBLE HYDROGEN BOND TO HOH 59
62: POSSIBLE HYDROGEN BONDS TO HOH 2, OG OF SER 85, CARBONYL OF ASP 87
63: POSSIBLE HYDROGEN BOND TO OG1 OF THR 89 / 64: POSSIBLE HYDROGEN BONDS TO CARBONYL OF GLY 16, HOH 43 / 65: POSSIBLE HYDROGEN BONDS TO HOH 65, N OF ARG 45 / 66: POSSIBLE HYDROGEN BONDS TO HOH 64, CARBONYL OF ARG 45 / 67: POSSIBLE HYDROGEN BOND TO HOH 50
68: POSSIBLE HYDROGEN BONDS TO HOH 67A, HOH 68, HOH 69, HOH 70 CARBONYL OF GLN 57
69: POSSIBLE HYDROGEN BONDS TO HOH 67, HOH 68, HOH 70
70: POSSIBLE HYDROGEN BONDS TO HOH 67, HOH 67A, CARBONYL OF ALA 107
71: POSSIBLE HYDROGEN BONDS TO HOH 67, N OF VAL 109
72: POSSIBLE HYDROGEN BONDS TO HOH 67, HOH 67A, OD1 AND OD2 OF ASP 52
73: POSSIBLE HYDROGEN BOND TO OD1 OF ASN 46 / 74: POSSIBLE HYDROGEN BOND TO CARBONYL OF ASN 46 / 75: POSSIBLE HYDROGEN BOND TO NZ OF LYS 96, HOH 75 / 76: POSSIBLE HYDROGEN BOND TO HOH 73 / 77: POSSIBLE HYDROGEN BOND TO N OF ASN 59 / 78: EXTENDED DENSITY NEAR CLEFT
79: POSSIBLE HYDROGEN BONDS TO CARBONYL OF GLY 49, OG1 OF THR 51, OG OF SER 60, ND2 OF ASP 66, NE OF ARG 68
81: NO CONTACT
82: POSSIBLE HYDROGEN BONDS TO CARBONYL OF ILE 98, N OF GLY 102, N OF ASN 103
83: POSSIBLE HYDROGEN BOND TO OD2 OF ASN 103, HOH 95 / 84: POSSIBLE HYDROGEN BOND TO CARBONYL OF THR 47
85: POSSIBLE HYDROGEN BONDS TO NE OF ARG 45, CARBONYL OF ASP 48, CARBONYL OF ARG 68
86: POSSIBLE HYDROGEN BONDS TO OH OF TYR 20, OG OF SER 100 / 88: POSSIBLE HYDROGEN BONDS TO NE OF ARG 21, OG OF SER 100 / 89: ON TWO-FOLD AXIS
90: POSSIBLE HYDROGEN BONDS TO HOH 94, NE1 OF TRP 62, HOH 95
91: POSSIBLE HYDROGEN BONDS TO HOH 93, NE OF ARG 61 / 92: POSSIBLE HYDROGEN BONDS TO HOH 82, HOH 93
93: POSSIBLE HYDROGEN BONDS TO OD1 OF ASN 65, N AND CARBONYL OF THR 69, OG OF SER 72, NEAR BAD PATCH
94: POSSIBLE HYDROGEN BOND TO CARBONYL OF CYS 76 / 95: POSSIBLE HYDROGEN BOND TO NE OF ARG 61 / 96: POSSIBLE HYDROGEN BOND TO HOH 100 / 97: POSSIBLE HYDROGEN BONDS TO HOH 99, HOH 101, HOH 102 / 98: POSSIBLE HYDROGEN BOND TO HOH 100 / 99: POSSIBLE HYDROGEN BONDS TO HOH 100, HOH 103 / 100: POSSIBLE HYDROGEN BONDS TO HOH 102, HOH 104 / 101: POSSIBLE HYDROGEN BOND TO HOH 103
Components on special symmetry positions
IDModelComponents
11A-218-

HOH

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Components

#1: Protein HEN EGG WHITE LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2 Å
Details: THE TEMPERATURE FACTOR FIELDS OF THIS ENTRY CONTAIN ELECTRON COUNTS INSTEAD, IN THE FORM THEY WERE DEPOSITED. THE WATER MOLECULES WERE REFINED AGAINST A DIFFERENCE- ELECTRON-DENSITY MAP ...Details: THE TEMPERATURE FACTOR FIELDS OF THIS ENTRY CONTAIN ELECTRON COUNTS INSTEAD, IN THE FORM THEY WERE DEPOSITED. THE WATER MOLECULES WERE REFINED AGAINST A DIFFERENCE- ELECTRON-DENSITY MAP OBTAINED USING THE COORDINATE SET DESIGNATED RS4 IN THE PAPER CITED IN THE JRNL RECORDS ABOVE.
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 101 1102

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