5JGN

Spin-Labeled T4 Lysozyme Construct I9V1

> Summary

Summary for 5JGN

Related5JGR 5JGU 5JGV 5JGX 5JGZ
DescriptorEndolysin (E.C.3.2.1.17)
Functional Keywordsspin label, epr, deer, hydrolase
Biological sourceEnterobacteria phage T4 sensu lato
Cellular locationHost cytoplasm  P00720
Total number of polymer chains1
Total molecular weight19145.58
Authors
Balo, A.R.,Feyrer, H.,Ernst, O.P. (deposition date: 2016-04-20, release date: 2017-02-15)
Primary citation
Balo, A.R.,Feyrer, H.,Ernst, O.P.
Spin-Labeled T4 Lysozyme Construct I9V1
To Be Published,
Experimental method
X-RAY DIFFRACTION (1.534 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.172400.7%2.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AEndolysinpolymer16418618.31
UniProt (P00720)
Pfam (PF00959)
Enterobacteria phage T4 sensu latoLysis protein, Lysozyme, Muramidase
CHLORIDE IONnon-polymer35.54
POTASSIUM IONnon-polymer39.11
S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioatenon-polymer251.31
PHOSPHATE IONnon-polymer95.01
waterwater18.0332

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight18618.3
Non-Polymers*Number of molecules7
Total molecular weight527.2
All*Total molecular weight19145.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.534 Å)

Cell axes59.82059.82095.672
Cell angles90.0090.00120.00
SpacegroupP 32 2 1
Resolution limits29.91 - 1.53
the highest resolution shell value1.572 - 1.534
R-factor0.153
R-work0.15170
the highest resolution shell value0.212
R-free0.17170
the highest resolution shell value0.278
RMSD bond length0.006
RMSD bond angle0.801

Data Collection Statistics

Resolution limits29.91 - 1.53
the highest resolution shell value -
Number of reflections30273
Completeness100.0
Redundancy2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP297

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
AC13binding site for residue CL A 201
ChainResidue
AASN132
ALYS135
AHOH391

AC26binding site for residue CL A 202
ChainResidue
ALYS124
ATHR142
AASN144
AARG145
AHOH378
AHOH624

AC36binding site for residue K A 203
ChainResidue
AGLU11
ATYR18
AHOH327
AHOH385
AHOH495
AHOH570

AC43binding site for residue CL A 204
ChainResidue
AHIS31
ALYS135
AHOH462

AC54binding site for residue V1A A 205
ChainResidue
AARG8
ACYS9
ALEU164
AHOH338

AC62binding site for residue CL A 206
ChainResidue
ALYS43
AASN55

AC78binding site for residue PO4 A 207
ChainResidue
ALYS19
AARG125
ATRP126
AASP127
AGLU128
AHOH310
AHOH397
AHOH433

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

site_idNumber of ResiduesDetails
V1A_5jgn_A_2055S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate binding site
ChainResidueligand
AGLU5V1A: S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate
AARG8-CYS9V1A: S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate
ATYR161V1A: S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate
ALEU164V1A: S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate

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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_FI11Proton donor. {ECO:0000255|HAMAP- Rule:MF_04110, ECO:0000269|PubMed:3382407}.
ChainResidueDetails
AGLU11

SWS_FT_FI21Nucleophile. {ECO:0000255|HAMAP- Rule:MF_04110, ECO:0000269|PubMed:1892846, ECO:0000269|PubMed:3382407}.
ChainResidueDetails
AASP20

SWS_FT_FI31N-acetyl-D-glucosamine; via amide nitrogen. {ECO:0000255|HAMAP- Rule:MF_04110, ECO:0000269|PubMed:8266098}.
ChainResidueDetails
ALEU32

SWS_FT_FI41N-acetyl-D-glucosamine; via carbonyl nitrogen. {ECO:0000255|HAMAP- Rule:MF_04110, ECO:0000269|PubMed:8266098}.
ChainResidueDetails
APHE104

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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