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- PDB-1dkk: BOBWHITE QUAIL LYSOZYME WITH NITRATE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1dkk
TitleBOBWHITE QUAIL LYSOZYME WITH NITRATE
ComponentsLYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL) / HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME
Function / homology
Function and homology information


lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
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 speciesColinus virginianus (northern bobwhite)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsJeffrey, P.D. / Sheriff, S.
CitationJournal: Proteins / Year: 1996
Title: Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment.
Authors: Chacko, S. / Silverton, E.W. / Smith-Gill, S.J. / Davies, D.R. / Shick, K.A. / Xavier, K.A. / Willson, R.C. / Jeffrey, P.D. / Chang, C.Y. / Sieker, L.C. / Sheriff, S.
History
DepositionJan 10, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)28,8266
Polymers28,5782
Non-polymers2484
Water2,774154
1
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3512
Polymers14,2891
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4754
Polymers14,2891
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.000, 62.600, 60.800
Angle α, β, γ (deg.)90.00, 91.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97169, 0.225451, -0.070642), (-0.215583, 0.968415, 0.125286), (0.096657, -0.10651, 0.989602)
Vector: 8.22, -3.09, 33.39)

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Components

#1: Protein LYSOZYME


Mass: 14289.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Colinus virginianus (northern bobwhite) / Cell: EGG / References: UniProt: P00700, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


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


Mass: 18.015 Da / Num. of mol.: 154 / 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

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 34 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMsodium acetate1drop
245 mg/mlBWQL1drop
30.625 mMformamide1drop
46 %(w/v)sodium nitrate1drop
510 mMsodium acetate1reservoir
61.25 mMformamide1reservoir
712 %(w/v)sodium nitrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 14910 / % possible obs: 85 % / Redundancy: 3 % / Rmerge(I) obs: 0.037
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 85 % / Num. measured all: 43399 / Rmerge(I) obs: 0.0367

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Processing

Software
NameClassification
MADNESdata collection
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementResolution: 1.9→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.157 -
obs-14283
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 16 154 2166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.6
X-RAY DIFFRACTIONt_dihedral_angle_d25
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg25
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_improper_angle_deg2.1

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