4NCJ - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSIS RAD50 R805E MUTATION WITH ADP BERYLLIUM FLOURIDE

Authors :   S. Classen, G. J. Williams, A. S. Arvai, R. S. Williams

Date :   24 Oct 13 (Deposition) - 05 Mar 14 (Release) - 02 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Adenosine Triphosphatase, Dna Repair, Dna Binding Protein, Fungal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. A. Deshpande, G. J. Williams, O. Limbo, R. S. Williams, J. Kuhnlein, J. H. Lee, S. Classen, G. Guenther, P. Russell, J. A. Tainer, T. T. Paull
Atp-Driven Rad50 Conformations Regulate Dna Tethering, End Resection, And Atm Checkpoint Signaling.
Embo J. V. 33 482 2014
PubMed-ID: 24493214 | Reference-DOI: 10.1002/EMBJ.201386100

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA2 (DE3)
	Expression System Taxid	:	469008
	Fragment	:	UNP RESIDUES 1-177 AND 726-882
	Gene	:	PF1167, RAD50
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	186497
	Strain	:	ATCC 43587 / DSM 3638 / JCM 8422 / VC1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	BEF	4	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
3	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	BEF	1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	BEF	1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	BEF	1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	BEF	1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:12 , SER A:13 , GLY A:33 , SER A:34 , GLY A:35 , LYS A:36 , SER A:37 , SER A:38 , GLU A:60 , THR A:62 , LYS A:63 , VAL A:64 , BEF A:902 , MG A:903 , HOH A:1011 , HOH A:1018 , HOH A:1045 , HOH A:1046 , HOH A:1070 , LYS C:763 , TYR C:764 , PHE C:791 , SER C:793 , GLU C:796	BINDING SITE FOR RESIDUE ADP A 901
02	AC2	SOFTWARE	ASN A:32 , GLY A:33 , LYS A:36 , GLN A:140 , ADP A:901 , MG A:903 , HOH A:1003 , HOH A:1053 , SER C:793 , GLY C:794 , GLY C:795	BINDING SITE FOR RESIDUE BEF A 902
03	AC3	SOFTWARE	SER A:37 , GLN A:140 , ADP A:901 , BEF A:902 , HOH A:1045 , HOH A:1053	BINDING SITE FOR RESIDUE MG A 903
04	AC4	SOFTWARE	ARG B:12 , SER B:13 , ASN B:32 , GLY B:33 , SER B:34 , GLY B:35 , LYS B:36 , SER B:37 , SER B:38 , GLU B:60 , THR B:62 , LYS B:63 , VAL B:64 , BEF B:902 , MG B:903 , HOH B:1003 , HOH B:1007 , HOH B:1043 , HOH B:1046 , HOH B:1071 , LYS D:763 , TYR D:764 , PHE D:791 , SER D:793 , GLU D:796	BINDING SITE FOR RESIDUE ADP B 901
05	AC5	SOFTWARE	ASN B:32 , GLY B:33 , LYS B:36 , GLN B:140 , ADP B:901 , MG B:903 , HOH B:1003 , HOH B:1012 , HOH B:1065 , SER D:793 , GLY D:794 , GLY D:795	BINDING SITE FOR RESIDUE BEF B 902
06	AC6	SOFTWARE	SER B:37 , GLN B:140 , ADP B:901 , BEF B:902 , HOH B:1003 , HOH B:1065	BINDING SITE FOR RESIDUE MG B 903
07	AC7	SOFTWARE	LYS A:763 , TYR A:764 , PHE A:791 , SER A:793 , GLU A:796 , ARG C:12 , SER C:13 , ASN C:32 , GLY C:33 , SER C:34 , GLY C:35 , LYS C:36 , SER C:37 , SER C:38 , GLU C:60 , THR C:62 , LYS C:63 , VAL C:64 , BEF C:902 , MG C:903 , HOH C:1001 , HOH C:1002 , HOH C:1030 , HOH C:1045 , HOH C:1053 , HOH C:1080	BINDING SITE FOR RESIDUE ADP C 901
08	AC8	SOFTWARE	SER A:793 , GLY A:794 , GLY A:795 , HOH A:1083 , ASN C:32 , GLY C:33 , LYS C:36 , GLN C:140 , ADP C:901 , MG C:903 , HOH C:1002 , HOH C:1023	BINDING SITE FOR RESIDUE BEF C 902
09	AC9	SOFTWARE	SER C:37 , GLN C:140 , ADP C:901 , BEF C:902 , HOH C:1001 , HOH C:1002	BINDING SITE FOR RESIDUE MG C 903
10	BC1	SOFTWARE	LYS B:763 , TYR B:764 , PHE B:791 , SER B:793 , GLU B:796 , ARG D:12 , SER D:13 , ASN D:32 , GLY D:33 , SER D:34 , GLY D:35 , LYS D:36 , SER D:37 , SER D:38 , GLU D:60 , THR D:62 , LYS D:63 , VAL D:64 , BEF D:902 , MG D:903 , HOH D:1004 , HOH D:1005 , HOH D:1028 , HOH D:1035 , HOH D:1058 , HOH D:1059	BINDING SITE FOR RESIDUE ADP D 901
11	BC2	SOFTWARE	SER B:793 , GLY B:794 , GLY B:795 , ASN D:32 , GLY D:33 , LYS D:36 , GLN D:140 , ADP D:901 , MG D:903 , HOH D:1004 , HOH D:1005 , HOH D:1024 , HOH D:1086	BINDING SITE FOR RESIDUE BEF D 902
12	BC3	SOFTWARE	SER D:37 , GLN D:140 , ADP D:901 , BEF D:902 , HOH D:1004 , HOH D:1005	BINDING SITE FOR RESIDUE MG D 903

(no "SS Bond" information available for 4NCJ)

Asymmetric Unit

No.	Residues
1	Trp A:49	-	Pro A:50
2	Trp B:49	-	Pro B:50
3	Trp C:49	-	Pro C:50
4	Glu C:783	-	Gly C:784
5	Trp D:49	-	Pro D:50

(no "SAP(SNP)/Variant" information available for 4NCJ)

(no "PROSITE Motif" information available for 4NCJ)

(no "Exon" information available for 4NCJ)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeee...eeeeee.....hhhhhhhhhhhhhhh.......hhhhhh.....eeeeeeeeee..eeeeeeeeee........eeeeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee....eeeeeee..eeehhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.eeeeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncj A   1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFELAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  ||   741       751       761       771       781       791       801       811       821       831       841       851       861       871       881 
                                                                                                                                                                                            163|                                                                                                                                                   
                                                                                                                                                                                             735

Chain B from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeee...eeeeee.....hhhhhhhhhhhhhhh.......hhhhhh.....eeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeee..eeehhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh....eeeeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncj B   1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFELAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   ||  741       751       761       771       781       791       801       811       821       831       841       851       861       871       881 
                                                                                                                                                                                             164|                                                                                                                                                  
                                                                                                                                                                                              736

Chain C from PDB  Type:PROTEIN  Length:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeee...eeeeee.....hhhhhhhhhhhhhhh.......hhhhhh.....eeeeeeeeee..eeeeeeeeee..hhhhheeeeeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhee.....hhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeee..eeehhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.eeeeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncj C   1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFELAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  ||   732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882
                                                                                                                                                                                            163|                                                                                                                                                            
                                                                                                                                                                                             726

Chain D from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeee...eeeeee.....hhhhhhhhhhhhhhh.......hhhhhh.....eeeeeeeeee..eeeeeeeeee..hhhhheeeeeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeee..eeehhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.eeeeeeee..eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncj D   1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFELAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   ||  731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881 
                                                                                                                                                                                             164|                                                                                                                                                            
                                                                                                                                                                                              726

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4NCJ)

(no "CATH Domain" information available for 4NCJ)

(no "Pfam Domain" information available for 4NCJ)

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	Cis Peptide Bonds
		Glu C:783 - Gly C:784	[ RasMol ]
		Trp A:49 - Pro A:50	[ RasMol ]
		Trp B:49 - Pro B:50	[ RasMol ]
		Trp C:49 - Pro C:50	[ RasMol ]
		Trp D:49 - Pro D:50	[ RasMol ]

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	RAD50_PYRFU \| P58301	:	1f2t 1f2u 1ii8 1l8d 1us8 3qkr 3qks 3qkt 3qku 4nch 4nci 4nck

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