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- PDB-1lma: PROTEIN HYDRATION AND WATER STRUCTURE: X-RAY ANALYSIS OF A CLOSEL... -

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Basic information

Entry
Database: PDB / ID: 1lma
TitlePROTEIN HYDRATION AND WATER STRUCTURE: X-RAY ANALYSIS OF A CLOSELY PACKED PROTEIN CRYSTAL WITH VERY LOW SOLVENT CONTENT
ComponentsHEN EGG WHITE LYSOZYME
KeywordsHYDROLASE(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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsMadhusudan / Kodandapani, R. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Protein hydration and water structure: X-ray analysis of a closely packed protein crystal with very low solvent content.
Authors: Madhusudan / Kodandapani, R. / Vijayan, M.
#1: Journal: Curr.Sci. / Year: 1991
Title: Rigid and Flexible Regions in Lysozyme and the Invariant Features in its Hydration Shell
Authors: Madhusudan / Vijayan, M.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Crystal Structure of Low Humidity Tetragonal Lysozyme at 2.1 Angstroms Resolution: Variability in Hydration Shell and its Structural Consequences
Authors: Kodandapani, R. / Suresh, C.G. / Vijayan, M.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1985
Title: Water-Mediated Transformations in Protein Crystals
Authors: Salunke, D.M. / Veerapandian, B. / Kodandapani, R. / Vijayan, M.
#4: Journal: Curr.Sci. / Year: 1984
Title: Water-Mediated Structural Transformations in a New Crystal Form of Ribonuclease A and Tetragonal Lysozyme
Authors: Salunke, D.M. / Veerapandian, B. / Vijayan, M.
History
DepositionAug 14, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEN EGG WHITE LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4553
Polymers14,3311
Non-polymers1242
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.900, 58.950, 31.330
Angle α, β, γ (deg.)90.00, 111.93, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: THE ELECTRON DENSITY OF SIDE CHAIN ATOMS OF GLN 121 IS TOO POOR TO ACCURATELY POSITION SIDE CHAIN ATOMS BEYOND CB.

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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: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 1.61 Å3/Da / Density % sol: 23.5 %
Crystal grow
*PLUS
pH: 4.5 / Method: unknown
Details: taken from Steinrauf, L.K. (1959). Acta Cryst. 12, 77.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %protein11
23 %sodium nitrate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.75 Å / Num. obs: 8288 / Observed criterion σ(I): 2 / Num. measured all: 43889 / Rmerge(I) obs: 0.061 / Biso Wilson estimate: 10 Å2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.75→10 Å / σ(F): 4 /
RfactorNum. reflection
obs0.175 7684
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 8 148 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.0910.12
X-RAY DIFFRACTIONp_singtor_nbd0.180.5
X-RAY DIFFRACTIONp_multtor_nbd0.2860.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1940.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.85
X-RAY DIFFRACTIONp_staggered_tor17.320
X-RAY DIFFRACTIONp_orthonormal_tor23.320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 10 Å / Num. reflection obs: 7684 / σ(F): 4 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS

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