4CEJ

Crystal structure of ADPNP-bound AddAB bound to Chi

> Summary

Summary for 4CEJ

Related4CEH 4CEI
DescriptorATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT A (E.C.3.1.-.-, 3.6.4.12), ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT B (E.C.3.1.-.-, 3.6.4.12)
Functional Keywordshydrolase-dna complex, helicase-nuclease, dna breaks, dna repair, single-stranded, dna-binding proteins, exodeoxyribonuclease v, exodeoxyribonucleases, homologous recombination, hydrolase/dna
Biological sourceBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
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Total number of polymer chains3
Total molecular weight298880.96
Authors
Krajewski, W.W.,Wilkinson, M.,Fu, X.,Cronin, N.B.,Wigley, D. (deposition date: 2013-11-11, release date: 2014-03-12, modification date: 2014-04-23)
Primary citation
Krajewski, W.W.,Fu, X.,Wilkinson, M.,Cronin, N.B.,Dillingham, M.S.,Wigley, D.B.
Structural Basis for Translocation by Addab Helicase-Nuclease and its Arrest at Chi Sites.
Nature, 508:416-, 2014
PubMed: 24670664
DOI: 10.1038/NATURE13037
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.24280.1%7.1%2.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT Apolymer1232141220.01
UniProt (P23478)
Pfam (PF00580)
Pfam (PF12705)
Pfam (PF13361)
BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168ATP-DEPENDENT HELICASE/NUCLEASE ADDA
BATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT Bpolymer1166134770.41
UniProt (P23477)
Pfam (PF12705)
BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168ATP-DEPENDENT HELICASE-NUCLEASE SUBUNIT B, ATP-DEPENDENT HELICASE/NUCLEASE ADDB
XDNApolymer7021477.91
SYNTHETIC CONSTRUCT
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTERnon-polymer506.22
MAGNESIUM IONnon-polymer24.32
IRON/SULFUR CLUSTERnon-polymer351.61
waterwater18.07

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight297468.3
Non-Polymers*Number of molecules5
Total molecular weight1412.6
All*Total molecular weight298881.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3 Å)
Cell axes77.437152.941125.244
Cell angles90.0094.3090.00
SpacegroupP 1 21 1
Resolution limits29.73 - 3.00
the highest resolution shell value3.049 - 3.000
R-factor0.2048
R-work0.20270
the highest resolution shell value0.311
R-free0.24340
the highest resolution shell value0.364
RMSD bond length0.004
RMSD bond angle0.774

Data Collection Statistics

Resolution limits35.55 - 3.00
the highest resolution shell value -
Number of reflections57963
Rmerge_l_obs0.050
the highest resolution shell value0.420
Completeness99.7
Redundancy3.8
the highest resolution shell value3.9
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
17.5

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
A0008408molecular_function3'-5' exonuclease activity
A0005524molecular_functionATP binding
A0004003molecular_functionATP-dependent DNA helicase activity
A0003690molecular_functiondouble-stranded DNA binding
A0000724biological_processdouble-strand break repair via homologous recombination
B0051539molecular_function4 iron, 4 sulfur cluster binding
B0008409molecular_function5'-3' exonuclease activity
B0005524molecular_functionATP binding
B0003690molecular_functiondouble-stranded DNA binding
B0004386molecular_functionhelicase activity
B0046872molecular_functionmetal ion binding
B0000724biological_processdouble-strand break repair via homologous recombination
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC120BINDING SITE FOR RESIDUE ANP A 2233
ChainResidue
ATHR10
AGLN15
AALA31
AALA32
AGLY33
ASER34
AGLY35
ALYS36
ATHR37
AALA38
AGLN441
APHE478
AARG479
ALYS573
AGLU800
AARG873
AHOH
AHOH
AHOH
AMG

AC25BINDING SITE FOR RESIDUE MG A 2234
ChainResidue
ATHR37
AHOH
AHOH
AHOH
AANP

AC35BINDING SITE FOR RESIDUE SF4 B 2160
ChainResidue
BCYS801
BPRO1112
BCYS1121
BCYS1124
BCYS1130

AC415BINDING SITE FOR RESIDUE ANP B 2161
ChainResidue
BSER10
BGLY11
BSER12
BGLY13
BLYS14
BTHR15
BLYS16
BTHR236
BGLU282
BARG283
BGLY600
BMET656
BHOH
BHOH
BMG

AC56BINDING SITE FOR RESIDUE MG B 2162
ChainResidue
BTHR15
BASP208
BHOH
BHOH
BHOH
BANP

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

site_idNumber of ResiduesDetails
ANP_4cej_A_223322PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER binding site
ChainResidueligand
ATHR10-THR12ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AGLN15ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AALA31-ALA38ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AARG76ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AGLU408ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AASP438ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AGLN441ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
APHE478-ARG479ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ALYS573ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AGLY798ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AGLU800ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AARG873ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

ANP_4cej_B_216118PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER binding site
ChainResidueligand
BARG9-LEU17ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BASP208ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BTHR236ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BGLU282-ARG283ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BTYR599-THR601ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BMET656ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BSER662ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

SF4_4cej_B_216012IRON/SULFUR CLUSTER binding site
ChainResidueligand
BCYS801SF4: IRON/SULFUR CLUSTER
BPHE803-SER804SF4: IRON/SULFUR CLUSTER
BILE1110SF4: IRON/SULFUR CLUSTER
BPRO1112SF4: IRON/SULFUR CLUSTER
BPRO1120-CYS1121SF4: IRON/SULFUR CLUSTER
BCYS1124SF4: IRON/SULFUR CLUSTER
BPHE1126-LYS1127SF4: IRON/SULFUR CLUSTER
BCYS1130SF4: IRON/SULFUR CLUSTER
BPHE1132SF4: IRON/SULFUR CLUSTER

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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 (Potential).
ChainResidueDetails
ANA*

SWS_FT_FI31ATP (Potential).
ChainResidueDetails
BNA*

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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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