1FNN

CRYSTAL STRUCTURE OF CDC6P FROM PYROBACULUM AEROPHILUM

> Summary

Summary for 1FNN

DescriptorCDC6P
Functional Keywordscdc6, cdc18, orc1, aaa protein, dna replication initation factor, cell cycle control factor, cell cycle
Biological sourcePyrobaculum aerophilum
Total number of polymer chains2
Total molecular weight89429.54
Authors
Liu, J.,Smith, C.L.,DeRyckere, D.,DeAngelis, K.,Martin, G.S.,Berger, J.M. (deposition date: 2000-08-22, release date: 2000-10-04, modification date: 2009-02-24)
Primary citation
Liu, J.,Smith, C.L.,DeRyckere, D.,DeAngelis, K.,Martin, G.S.,Berger, J.M.
Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control.
Mol.Cell, 6:637-648, 2000
PubMed: 11030343
DOI: 10.1016/S1097-2765(00)00062-9
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliersRSRZ outliers80.1%5.5%1.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

More Biological unit images

Molmil generated image of 1fnn
no rotation
Molmil generated image of 1fnn
rotated about x axis by 90°
Molmil generated image of 1fnn
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 (1fnn.pdb1.gz [67.2 KB])
Coordinate files for Biological unit (1fnn.pdb2.gz [67.66 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BCELL DIVISION CONTROL PROTEIN 6polymer38944263.32
UniProt (Q8ZYK1)
Pfam (PF09079)
Pfam (PF13401)
Pyrobaculum aerophilumCDC6P
MAGNESIUM IONnon-polymer24.32
ADENOSINE-5'-DIPHOSPHATEnon-polymer427.22
waterwater18.0327

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight88526.5
Non-Polymers*Number of molecules4
Total molecular weight903.0
All*Total molecular weight89429.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Cell axes132.070132.07082.200
Cell angles90.0090.00120.00
SpacegroupP 31
Resolution limits20.00 - 2.00
the highest resolution shell value -
R-work0.22100
R-free0.25700
RMSD bond length0.014
RMSD bond angle1.900

Data Collection Statistics

Resolution limits100.00 - 2.00
the highest resolution shell value -
Number of reflections106577
Rmerge_l_obs0.057*
the highest resolution shell value0.285*
Completeness98.4
the highest resolution shell value98.7*
Redundancy2.5
the highest resolution shell value2.5
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.5 (8.5*)298K*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11reservoirMPD6 (%)
21reservoirmagnesium acetate40 (mM)
31reservoirTris-HCl20 (mM)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005524molecular_functionATP binding
A0051301biological_processcell division
A0006260biological_processDNA replication
B0005524molecular_functionATP binding
B0051301biological_processcell division
B0006260biological_processDNA replication
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16BINDING SITE FOR RESIDUE MG A 390
ChainResidue
ATHR58
AADP
AHOH
AHOH
AHOH
AHOH

AC26BINDING SITE FOR RESIDUE MG B 391
ChainResidue
BTHR58
BADP
BHOH
BHOH
BHOH
BHOH

AC325BINDING SITE FOR RESIDUE ADP A 398
ChainResidue
ATYR14
APRO16
ALEU19
APRO20
AARG22
AGLY54
ATHR55
AGLY56
ALYS57
ATHR58
AVAL59
ATYR193
AILE201
AARG205
AALA240
AILE244
AMG
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH

AC424BINDING SITE FOR RESIDUE ADP B 399
ChainResidue
BTYR14
BLEU19
BPRO20
BARG22
BGLY54
BTHR55
BGLY56
BLYS57
BTHR58
BVAL59
BTYR193
BILE201
BARG205
BALA240
BILE244
BMG
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH

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

site_idNumber of ResiduesDetails
ADP_1fnn_A_39823ADENOSINE-5'-DIPHOSPHATE binding site
ChainResidueligand
ASER10-PRO11ADP: ADENOSINE-5'-DIPHOSPHATE
ATYR13ADP: ADENOSINE-5'-DIPHOSPHATE
APRO15ADP: ADENOSINE-5'-DIPHOSPHATE
AARG17-PRO19ADP: ADENOSINE-5'-DIPHOSPHATE
AARG21ADP: ADENOSINE-5'-DIPHOSPHATE
AARG51-THR59ADP: ADENOSINE-5'-DIPHOSPHATE
ATYR192ADP: ADENOSINE-5'-DIPHOSPHATE
AILE200ADP: ADENOSINE-5'-DIPHOSPHATE
AARG204ADP: ADENOSINE-5'-DIPHOSPHATE
AALA239-ARG240ADP: ADENOSINE-5'-DIPHOSPHATE
AILE243ADP: ADENOSINE-5'-DIPHOSPHATE

ADP_1fnn_B_39923ADENOSINE-5'-DIPHOSPHATE binding site
ChainResidueligand
BSER10-PRO11ADP: ADENOSINE-5'-DIPHOSPHATE
BTYR13ADP: ADENOSINE-5'-DIPHOSPHATE
BPRO15ADP: ADENOSINE-5'-DIPHOSPHATE
BARG17-PRO19ADP: ADENOSINE-5'-DIPHOSPHATE
BARG21ADP: ADENOSINE-5'-DIPHOSPHATE
BARG51-THR59ADP: ADENOSINE-5'-DIPHOSPHATE
BTYR192ADP: ADENOSINE-5'-DIPHOSPHATE
BILE200ADP: ADENOSINE-5'-DIPHOSPHATE
BARG204ADP: ADENOSINE-5'-DIPHOSPHATE
BALA239-ARG240ADP: ADENOSINE-5'-DIPHOSPHATE
BILE243ADP: ADENOSINE-5'-DIPHOSPHATE

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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_FI13ADP.
ChainResidueDetails
ATYR193
AILE201
AARG205

SWS_FT_FI23ADP.
ChainResidueDetails
ANA*
ANA*
ANA*

SWS_FT_FI33ADP.
ChainResidueDetails
BTYR193
BILE201
BARG205

SWS_FT_FI43ADP.
ChainResidueDetails
BNA*
BNA*
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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