4BXO

Architecture and DNA recognition elements of the Fanconi anemia FANCM- FAAP24 complex

> Summary

Summary for 4BXO

DescriptorFANCONI ANEMIA GROUP M PROTEIN (E.C.3.6.4.13), FANCONI ANEMIA-ASSOCIATED PROTEIN OF 24 KDA
Functional Keywordshydrolase-dna complex, dna binding, pseudo-nuclease, hydrolase/dna
Biological sourceHOMO SAPIENS (HUMAN)
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Cellular locationNucleus Q8IYD8 Q9BTP7
Total number of polymer chains4
Total molecular weight59690.05
Authors
Coulthard, R.,Deans, A.,Swuec, P.,Bowles, M.,Purkiss, A.,Costa, A.,West, S.,McDonald, N. (deposition date: 2013-07-15, release date: 2013-08-28, modification date: 2013-09-25)
Primary citation
Coulthard, R.,Deans, A.J.,Swuec, P.,Bowles, M.,Costa, A.,West, S.C.,Mcdonald, N.Q.
Architecture and DNA Recognition Elements of the Fanconi Anemia Fancm-Faap24 Complex.
Structure, 21:1648-, 2013
PubMed: 23932590
DOI: 10.1016/J.STR.2013.07.006
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.15 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.281503.6%5.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AFANCONI ANEMIA GROUP M PROTEINpolymer25428772.11
UniProt (Q8IYD8)
Pfam (PF02732)
HOMO SAPIENS (HUMAN)@PDBjPROTEIN FACM, ATP-DEPENDENT RNA HELICASE FANCM, FANCONI ANE MIA-ASSOCIATED POLYPEPTIDE OF 250 KDA, FAAP250, PROTEIN HEF ORTHOL OG, FANCM
BFANCONI ANEMIA-ASSOCIATED PROTEIN OF 24 KDApolymer21724051.11
UniProt (Q9BTP7)
Pfam (PF12826)
HOMO SAPIENS (HUMAN)@PDBjFAAP24
H5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*AP*TP*CP)-3'polymer113413.31
SYNTHETIC CONSTRUCT
I5'-D(*GP*AP*TP*GP*AP*TP*GP*CP*TP*GP*CP)-3'polymer113293.21
SYNTHETIC CONSTRUCT
CALCIUM IONnon-polymer40.14
waterwater18.0100

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight59529.7
Non-Polymers*Number of molecules4
Total molecular weight160.3
All*Total molecular weight59690.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.15 Å)
Cell axes125.100125.10074.760
Cell angles90.0090.0090.00
SpacegroupP 41 21 2
Resolution limits25.43 - 2.15
the highest resolution shell value2.206 - 2.150
R-factor0.20615
R-work0.20360
the highest resolution shell value0.209
R-free0.25523
the highest resolution shell value0.269
RMSD bond length0.023
RMSD bond angle1.983

Data Collection Statistics

Resolution limits30.34 - 2.15
the highest resolution shell value -
Number of reflections32846
Rmerge_l_obs0.060
the highest resolution shell value0.370
Completeness100.0
Redundancy10
the highest resolution shell value9.9
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
18

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
A0071821cellular_componentFANCM-MHF complex
A0043240cellular_componentFanconi anaemia nuclear complex
A0005654cellular_componentnucleoplasm
A0005524molecular_functionATP binding
A0003682molecular_functionchromatin binding
A0003677molecular_functionDNA binding
A0004386molecular_functionhelicase activity
A0004518molecular_functionnuclease activity
A0006281biological_processDNA repair
A0036297biological_processinterstrand cross-link repair
A0031297biological_processreplication fork processing
A0000712biological_processresolution of meiotic recombination intermediates
B0043240cellular_componentFanconi anaemia nuclear complex
B0043231cellular_componentintracellular membrane-bounded organelle
B0005654cellular_componentnucleoplasm
B0003682molecular_functionchromatin binding
B0003677molecular_functionDNA binding
B0006281biological_processDNA repair
B0036297biological_processinterstrand cross-link repair
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE CA A 2050
ChainResidue
AASP60
AGLU70
AARG71
AHOH

AC24BINDING SITE FOR RESIDUE CA B 1215
ChainResidue
BGLU46
BASP47
BASP47
BHOH

AC35BINDING SITE FOR RESIDUE CA B 1216
ChainResidue
BGLN167
BVAL172
BHOH
BHOH
IDT7

AC43BINDING SITE FOR RESIDUE CA B 1217
ChainResidue
BGLU199
BVAL202
HDA11

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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_FI11ATP (Probable).
ChainResidueDetails
ANA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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