1QGH

THE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LISTERIA INNOCUA, REVEALS A NOVEL INTERSUBUNIT IRON BINDING SITE.

> Summary

Summary for 1QGH

DescriptorNON-HEME IRON-CONTAINING FERRITIN
Functional Keywordsferritin, metal transport
Biological sourceListeria innocua
Cellular locationCytoplasm (By similarity) P80725
Total number of polymer chains12
Total molecular weight217518.48
Authors
Ilari, A.,Stefanini, S.,Chiancone, E.,Tsernoglou, D. (deposition date: 1999-04-27, release date: 2000-01-14, modification date: 2009-02-24)
Primary citation
Ilari, A.,Stefanini, S.,Chiancone, E.,Tsernoglou, D.
The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site.
Nat.Struct.Biol., 7:38-43, 2000
PubMed: 10625425
DOI: 10.1038/71236
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.35 Å)
?

Structure validation

ClashscoreRamachandran outliersSidechain outliers1708.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1qgh
no rotation
Molmil generated image of 1qgh
rotated about x axis by 90°
Molmil generated image of 1qgh
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, D, E...NON-HEME IRON-CONTAINING FERRITINpolymer15618070.712
UniProt (P80725)
Pfam (PF00210)
Listeria innocua
FE (III) IONnon-polymer55.812
waterwater18.0479

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains12
Total molecular weight216848.3
Non-Polymers*Number of molecules12
Total molecular weight670.2
All*Total molecular weight217518.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.35 Å)

Cell axes87.540137.500173.360
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits10.00 - 2.35
the highest resolution shell value -
R-work0.21900
RMSD bond length0.012
RMSD bond angle2.039 (14.698*)

Data Collection Statistics

Resolution limits30.00 - 2.35
the highest resolution shell value -
Number of reflections80150
Rmerge_l_obs0.077*
Completeness91.3
Redundancy3.8

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1Vapor diffusion, sitting drop*5.8293*K*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein7 (mg/ml)
21reservoirMES0.1 (M)
31reservoirPEG100019-25 (%)
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0008199molecular_functionferric iron binding
A0016722molecular_functionoxidoreductase activity, oxidizing metal ions
A0006879biological_processcellular iron ion homeostasis
A0006950biological_processresponse to stress
B0005737cellular_componentcytoplasm
B0008199molecular_functionferric iron binding
B0016722molecular_functionoxidoreductase activity, oxidizing metal ions
B0006879biological_processcellular iron ion homeostasis
B0006950biological_processresponse to stress
C0005737cellular_componentcytoplasm
C0008199molecular_functionferric iron binding
C0016722molecular_functionoxidoreductase activity, oxidizing metal ions
C0006879biological_processcellular iron ion homeostasis
C0006950biological_processresponse to stress
D0005737cellular_componentcytoplasm
D0008199molecular_functionferric iron binding
D0016722molecular_functionoxidoreductase activity, oxidizing metal ions
D0006879biological_processcellular iron ion homeostasis
D0006950biological_processresponse to stress
E0005737cellular_componentcytoplasm
E0008199molecular_functionferric iron binding
E0016722molecular_functionoxidoreductase activity, oxidizing metal ions
E0006879biological_processcellular iron ion homeostasis
E0006950biological_processresponse to stress
F0005737cellular_componentcytoplasm
F0008199molecular_functionferric iron binding
F0016722molecular_functionoxidoreductase activity, oxidizing metal ions
F0006879biological_processcellular iron ion homeostasis
F0006950biological_processresponse to stress
G0005737cellular_componentcytoplasm
G0008199molecular_functionferric iron binding
G0016722molecular_functionoxidoreductase activity, oxidizing metal ions
G0006879biological_processcellular iron ion homeostasis
G0006950biological_processresponse to stress
H0005737cellular_componentcytoplasm
H0008199molecular_functionferric iron binding
H0016722molecular_functionoxidoreductase activity, oxidizing metal ions
H0006879biological_processcellular iron ion homeostasis
H0006950biological_processresponse to stress
I0005737cellular_componentcytoplasm
I0008199molecular_functionferric iron binding
I0016722molecular_functionoxidoreductase activity, oxidizing metal ions
I0006879biological_processcellular iron ion homeostasis
I0006950biological_processresponse to stress
J0005737cellular_componentcytoplasm
J0008199molecular_functionferric iron binding
J0016722molecular_functionoxidoreductase activity, oxidizing metal ions
J0006879biological_processcellular iron ion homeostasis
J0006950biological_processresponse to stress
K0005737cellular_componentcytoplasm
K0008199molecular_functionferric iron binding
K0016722molecular_functionoxidoreductase activity, oxidizing metal ions
K0006879biological_processcellular iron ion homeostasis
K0006950biological_processresponse to stress
L0005737cellular_componentcytoplasm
L0008199molecular_functionferric iron binding
L0016722molecular_functionoxidoreductase activity, oxidizing metal ions
L0006879biological_processcellular iron ion homeostasis
L0006950biological_processresponse to stress
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
ASA5IRON-BINDING SITE
ChainResidue
AGLU62
AASP58
AHIS31
AASP47
AHIS43

ASB5IRON-BINDING SITE
ChainResidue
BGLU62
BASP58
BHIS31
BASP47
BHIS43

ASC5IRON-BINDING SITE
ChainResidue
CGLU62
CASP58
CHIS31
CASP47
CHIS43

ASD5IRON-BINDING SITE
ChainResidue
DGLU62
DASP58
DHIS31
DASP47
DHIS43

ASE5IRON-BINDING SITE
ChainResidue
EGLU62
EASP58
EHIS31
EASP47
EHIS43

ASF5IRON-BINDING SITE
ChainResidue
FGLU62
FASP58
FHIS31
FASP47
FHIS43

ASG5IRON-BINDING SITE
ChainResidue
GGLU62
GASP58
GHIS31
GASP47
GHIS43

ASH5IRON-BINDING SITE
ChainResidue
HGLU62
HASP58
HHIS31
HASP47
HHIS43

ASI5IRON-BINDING SITE
ChainResidue
IGLU62
IASP58
IHIS31
IASP47
IHIS43

ASJ5IRON-BINDING SITE
ChainResidue
JGLU62
JASP58
JHIS31
JASP47
JHIS43

ASK5IRON-BINDING SITE
ChainResidue
KGLU62
KASP58
KHIS31
KASP47
KHIS43

ASL5IRON-BINDING SITE
ChainResidue
LGLU62
LASP58
LHIS31
LASP47
LHIS43

AC14BINDING SITE FOR RESIDUE FE A 157
ChainResidue
EHIS31
EHOH197
GASP58
GGLU62

AC23BINDING SITE FOR RESIDUE FE B 157
ChainResidue
EASP58
EGLU62
GHIS31

AC34BINDING SITE FOR RESIDUE FE C 157
ChainResidue
AASP58
AGLU62
CHIS31
CASP47

AC44BINDING SITE FOR RESIDUE FE D 157
ChainResidue
AHIS31
AASP47
CASP58
CGLU62

AC53BINDING SITE FOR RESIDUE FE E 157
ChainResidue
IASP58
IGLU62
KHIS31

AC63BINDING SITE FOR RESIDUE FE F 157
ChainResidue
FHIS31
HASP58
HGLU62

AC75BINDING SITE FOR RESIDUE FE G 157
ChainResidue
JASP58
JGLU62
JHOH161
LHIS31
LASP47

AC84BINDING SITE FOR RESIDUE FE H 157
ChainResidue
JHIS31
LASP58
LGLU62
LHOH158

AC93BINDING SITE FOR RESIDUE FE I 157
ChainResidue
IHIS31
KASP58
KGLU62

BC13BINDING SITE FOR RESIDUE FE J 157
ChainResidue
BASP58
BGLU62
DHIS31

BC23BINDING SITE FOR RESIDUE FE K 157
ChainResidue
FASP58
FGLU62
HHIS31

BC33BINDING SITE FOR RESIDUE FE L 157
ChainResidue
BHIS31
DASP58
DGLU62

?

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

site_idNumber of ResiduesDetails
?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS0081912Dps protein family signature 2. [LIVMFY]-[DH]-x-[LIVM]-[GA]-E-R-x(3)-[LIF]-[GDN]-x(2)-[PA]
ChainResidueDetails
ANA*
BNA*
CNA*
DNA*
ENA*
FNA*
GNA*
HNA*
INA*
JNA*
KNA*
LNA*

PS0081812Dps protein family signature 1. H-[FW]-x-[LIVM]-x-G-x(5)-[LV]-H-x(3)-[DE]
ChainResidueDetails
ANA*
BNA*
CNA*
DNA*
ENA*
FNA*
GNA*
HNA*
INA*
JNA*
KNA*
LNA*

?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
?

Catalytic Information from CSA

site_idNumber of ResiduesDetails
?

Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2016 Protein Data Bank Japan