5GWB

Hen Egg White Lysozyme native crystals soaked for 2 hours in precipitant solution containing 1 M guanidine hydrochloride and 25% glycerol, before data collection

> Summary

Summary for 5GWB

DescriptorLysozyme C, CHLORIDE ION, GUANIDINE, ... (4 entities in total)
Functional Keywordsprotein unfolding, soaking, hydrolase
Biological sourceGallus gallus (Chicken)
Cellular locationSecreted P00698
Total number of polymer chains1
Total molecular weight14685.63
Authors
Hosur, M.V.,Kini, R.M.,Yeow, C. (deposition date: 2016-09-10, release date: 2017-09-13)
Primary citation
Hosur, M.V.,Kini, R.M.,Yeow, C.
Hen Egg White Lysozyme native crystals soaked for 2 hours in precipitant solution containing 1 M guanidine hydrochloride and 25% glycerol, before data collection
To Be Published,
Experimental method
X-RAY DIFFRACTION (2.001 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.23312000.8%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5gwb
no rotation
Molmil generated image of 5gwb
rotated about x axis by 90°
Molmil generated image of 5gwb
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ALysozyme Cpolymer12914331.21
UniProt (P00698)
Gallus gallus (Chicken)1,4-beta-N-acetylmuramidase C,Allergen Gal d IV
CHLORIDE IONnon-polymer35.55
GUANIDINEnon-polymer59.13
waterwater18.0124

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight14331.2
Non-Polymers*Number of molecules8
Total molecular weight354.5
All*Total molecular weight14685.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.001 Å)

Cell axes77.36077.36036.690
Cell angles90.0090.0090.00
SpacegroupP 43 21 2
Resolution limits33.15 - 2.00
the highest resolution shell value2.290 - 2.001
R-factor0.1841
R-work0.18160
the highest resolution shell value0.208
R-free0.23310
the highest resolution shell value0.253
RMSD bond length0.008
RMSD bond angle1.075

Data Collection Statistics

Resolution limits33.20 - 2.00
the highest resolution shell value -
Number of reflections7861
Completeness99.1
Redundancy4

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP4.5300

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC12binding site for residue CL A 201
ChainResidue
AARG73
AASN74

AC23binding site for residue CL A 203
ChainResidue
AARG14
AHIS15
AILE88

AC32binding site for residue CL A 204
ChainResidue
AASN59
ATRP63

AC42binding site for residue CL A 205
ChainResidue
ATYR23
AASN113

AC55binding site for residue GAI A 206
ChainResidue
AARG61
AILE124
ACYS127
AHOH317
AHOH371

AC66binding site for residue GAI A 207
ChainResidue
AGLN57
AILE58
AASN59
ATRP63
AALA107
AHOH368

AC78binding site for residue GAI A 208
ChainResidue
ATHR43
ATHR43
AASN44
AASN44
AARG45
AARG45
AHOH342
AHOH342

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
GAI_5gwb_A_2085GUANIDINE binding site
ChainResidueligand
ATHR43-ARG45GAI: GUANIDINE
ATHR51GAI: GUANIDINE
AARG68GAI: GUANIDINE

GAI_5gwb_A_2079GUANIDINE binding site
ChainResidueligand
AASP52GAI: GUANIDINE
ALEU56-ASN59GAI: GUANIDINE
ATRP63GAI: GUANIDINE
AILE98GAI: GUANIDINE
AALA107-TRP108GAI: GUANIDINE

GAI_5gwb_A_2066GUANIDINE binding site
ChainResidueligand
AILE124-LEU129GAI: GUANIDINE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI12
ChainResidueDetails
AGLU35
AASP52

SWS_FT_FI21Substrate.
ChainResidueDetails
AASP101

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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