4M6D

Crystal structure of the aptamer minF-lysozyme complex.

> Summary

Summary for 4M6D

Related4M4O
DescriptorLysozyme C (E.C.3.2.1.17)
Functional Keywordsstructural genomics, protein structure initiative, nysgrc, psi-biology, new york structural genomics research consortium, hydrolase-rna complex, hydrolase/rna
Biological sourceGallus gallus (bantam,chickens)
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Cellular locationSecreted P00698
Total number of polymer chains12
Total molecular weight173118.07
Authors
Primary citation
Malashkevich, V.N.,Padlan, F.C..,Toro, R.,Girvin, M.,Almo, S.C.
Crystal structure of the aptamer minF-lysozyme complex.
To be Published,
Experimental method
X-RAY DIFFRACTION (2.68 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone0.213180.4%7.9%15.7%0.29MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4m6d
no rotation
Molmil generated image of 4m6d
rotated about x axis by 90°
Molmil generated image of 4m6d
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 4m6d
no rotation
Molmil generated image of 4m6d
rotated about x axis by 90°
Molmil generated image of 4m6d
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (4m6d.pdb1.gz [85.31 KB])
Coordinate files for Biological unit (4m6d.pdb2.gz [85.86 KB])
Coordinate files for Biological unit (4m6d.pdb3.gz [85.57 KB])
Coordinate files for Biological unit (4m6d.pdb4.gz [85.5 KB])
Coordinate files for Biological unit (4m6d.pdb5.gz [84.62 KB])
Coordinate files for Biological unit (4m6d.pdb6.gz [86.32 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, C, E, G, I...Lysozyme Cpolymer12914331.26
UniProt (P00698)
Pfam (PF00062)
Gallus gallus (bantam chickens)@PDBj1,4-beta-N-acetylmuramidase C, Allergen Gal d IV
B, D, F, H, J...aptamerpolymer4514521.86
waterwater18.069

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains12
Total molecular weight173118.1
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight173118.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.68 Å)

Cell axes43.914132.289131.539
Cell angles118.5996.3996.27
SpacegroupP 1
Resolution limits38.04 - 2.68
the highest resolution shell value2.754 - 2.685
R-factor0.16832
R-work0.16549
the highest resolution shell value0.196
R-free0.21600
the highest resolution shell value0.277
RMSD bond length0.013
RMSD bond angle1.421

Data Collection Statistics

Resolution limits50.00 - 2.68
the highest resolution shell value -
Number of reflections67209
Rmerge_l_obs0.067
the highest resolution shell value0.629
Completeness94.9
Redundancy1.9
the highest resolution shell value1.8

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7298

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
A0005783cellular_componentendoplasmic reticulum
A0070062cellular_componentextracellular exosome
A0005615cellular_componentextracellular space
A0016231molecular_functionbeta-N-acetylglucosaminidase activity
A0042802molecular_functionidentical protein binding
A0003796molecular_functionlysozyme activity
A0051672biological_processcatabolism by organism of cell wall peptidoglycan in other organism
A0016998biological_processcell wall macromolecule catabolic process
A0019835biological_processcytolysis
A0042742biological_processdefense response to bacterium
A0050829biological_processdefense response to Gram-negative bacterium
A0050830biological_processdefense response to Gram-positive bacterium
A0001895biological_processretina homeostasis
C0005783cellular_componentendoplasmic reticulum
C0070062cellular_componentextracellular exosome
C0005615cellular_componentextracellular space
C0016231molecular_functionbeta-N-acetylglucosaminidase activity
C0042802molecular_functionidentical protein binding
C0003796molecular_functionlysozyme activity
C0051672biological_processcatabolism by organism of cell wall peptidoglycan in other organism
C0016998biological_processcell wall macromolecule catabolic process
C0019835biological_processcytolysis
C0042742biological_processdefense response to bacterium
C0050829biological_processdefense response to Gram-negative bacterium
C0050830biological_processdefense response to Gram-positive bacterium
C0001895biological_processretina homeostasis
E0005783cellular_componentendoplasmic reticulum
E0070062cellular_componentextracellular exosome
E0005615cellular_componentextracellular space
E0016231molecular_functionbeta-N-acetylglucosaminidase activity
E0042802molecular_functionidentical protein binding
E0003796molecular_functionlysozyme activity
E0051672biological_processcatabolism by organism of cell wall peptidoglycan in other organism
E0016998biological_processcell wall macromolecule catabolic process
E0019835biological_processcytolysis
E0042742biological_processdefense response to bacterium
E0050829biological_processdefense response to Gram-negative bacterium
E0050830biological_processdefense response to Gram-positive bacterium
E0001895biological_processretina homeostasis
G0005783cellular_componentendoplasmic reticulum
G0070062cellular_componentextracellular exosome
G0005615cellular_componentextracellular space
G0016231molecular_functionbeta-N-acetylglucosaminidase activity
G0042802molecular_functionidentical protein binding
G0003796molecular_functionlysozyme activity
G0051672biological_processcatabolism by organism of cell wall peptidoglycan in other organism
G0016998biological_processcell wall macromolecule catabolic process
G0019835biological_processcytolysis
G0042742biological_processdefense response to bacterium
G0050829biological_processdefense response to Gram-negative bacterium
G0050830biological_processdefense response to Gram-positive bacterium
G0001895biological_processretina homeostasis
I0005783cellular_componentendoplasmic reticulum
I0070062cellular_componentextracellular exosome
I0005615cellular_componentextracellular space
I0016231molecular_functionbeta-N-acetylglucosaminidase activity
I0042802molecular_functionidentical protein binding
I0003796molecular_functionlysozyme activity
I0051672biological_processcatabolism by organism of cell wall peptidoglycan in other organism
I0016998biological_processcell wall macromolecule catabolic process
I0019835biological_processcytolysis
I0042742biological_processdefense response to bacterium
I0050829biological_processdefense response to Gram-negative bacterium
I0050830biological_processdefense response to Gram-positive bacterium
I0001895biological_processretina homeostasis
K0005783cellular_componentendoplasmic reticulum
K0070062cellular_componentextracellular exosome
K0005615cellular_componentextracellular space
K0016231molecular_functionbeta-N-acetylglucosaminidase activity
K0042802molecular_functionidentical protein binding
K0003796molecular_functionlysozyme activity
K0051672biological_processcatabolism by organism of cell wall peptidoglycan in other organism
K0016998biological_processcell wall macromolecule catabolic process
K0019835biological_processcytolysis
K0042742biological_processdefense response to bacterium
K0050829biological_processdefense response to Gram-negative bacterium
K0050830biological_processdefense response to Gram-positive bacterium
K0001895biological_processretina homeostasis
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Functional Information from PDB Data

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

site_idNumber of ResiduesDetails
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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

SWS_FT_FI32
ChainResidueDetails
CGLU35
CASP52

SWS_FT_FI41Substrate.
ChainResidueDetails
CASP101

SWS_FT_FI52
ChainResidueDetails
EGLU35
EASP52

SWS_FT_FI61Substrate.
ChainResidueDetails
EASP101

SWS_FT_FI72
ChainResidueDetails
GGLU35
GASP52

SWS_FT_FI81Substrate.
ChainResidueDetails
GASP101

SWS_FT_FI92
ChainResidueDetails
IGLU35
IASP52

SWS_FT_FI101Substrate.
ChainResidueDetails
IASP101

SWS_FT_FI112
ChainResidueDetails
KGLU35
KASP52

SWS_FT_FI121Substrate.
ChainResidueDetails
KASP101

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb4m6d.ent.gz (507.47 KB)
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all (no-compress)pdb4m6d.ent (1.84 MB)
header onlypdb4m6d.ent.gz (10.14 KB)
Display
PDBx/mmCIF4m6d.cif.gz (613.26 KB)
PDBMLall4m6d.xml.gz (922.67 KB)
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no-atom4m6d-noatom.xml.gz (56.96 KB)
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ext-atom4m6d-extatom.xml.gz (271.04 KB)
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PDBMLplusall4m6d-plus.xml.gz (924.96 KB)
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no-atom4m6d-plus-noatom.xml.gz (59.26 KB)
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add only4m6d-add.xml.gz (2.29 KB)
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RDF4m6d.rdf.gz (94.99 KB)
Display
Structure factorsr4m6dsf.ent.gz (509.39 KB)
Biological unit (PDB format)4m6d.pdb1.gz (85.31 KB) (A,B)
*author defined assembly, 2 molecule(s) (dimeric)
Display
4m6d.pdb2.gz (85.86 KB) (C,D)
*author defined assembly, 2 molecule(s) (dimeric)
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4m6d.pdb3.gz (85.57 KB) (E,F)
*author defined assembly, 2 molecule(s) (dimeric)
Display
4m6d.pdb4.gz (85.5 KB) (G,H)
*author defined assembly, 2 molecule(s) (dimeric)
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4m6d.pdb5.gz (84.62 KB) (I,J)
*author defined assembly, 2 molecule(s) (dimeric)
Display
4m6d.pdb6.gz (86.32 KB) (K,L)
*author defined assembly, 2 molecule(s) (dimeric)
Display
Validation reportsPDF4m6d​_validation.pdf.gz (364.99 KB)
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PDF-full4m6d​_full​_validation.pdf.gz (414.39 KB)
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XML4m6d​_validation.xml.gz (43.84 KB)
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PNG4m6d​_multipercentile​_validation.png.gz (175.38 KB)
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SVG4m6d​_multipercentile​_validation.svg.gz (1020 B)
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Sequence (fasta)4m6d​_seq.txt
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