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Title :   CRYSTAL STRUCTURE OF THE METAL-DEPENDENT LIPOPROTEIN YCDH FROM BACILLUS SUBTILIS, NORTHEAST STRUCTURAL GENOMICS TARGET SR583

Authors :   F. Forouhar, W. Zhou, J. Seetharaman, C. X. Chen, Y. Fang, K. Cunningham, L. -C. Ma, H. Janjua, R. Xiao, M. C. Baran, J. Liu, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)

Date :   28 Nov 06 (Deposition) - 12 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Alpha-Beta Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Forouhar, W. Zhou, J. Seetharaman, C. X. Chen, Y. Fang, K. Cunningham, L. -C. Ma, H. Janjua, R. Xiao, M. C. Baran, J. Liu, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Metal-Dependent Lipoprotein Ycdh From Bacillus Subtilis, Northeast Structural Genomics Target Sr583
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - YCDH
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 22-319
	Gene	:	YCDH, LOCUS_TAG=BSU02850
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 14)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:51 , HIS A:128 , GLU A:267 , HOH A:411	BINDING SITE FOR RESIDUE MN A 401
2	AC2	SOFTWARE	HIS B:51 , HIS B:128 , GLU B:267 , HOH B:423	BINDING SITE FOR RESIDUE MN B 401

(no "SS Bond" information available for 2O1E)

(no "Cis Peptide Bond" information available for 2O1E)

(no "SAP(SNP)/Variant" information available for 2O1E)

(no "PROSITE Motif" information available for 2O1E)

(no "Exon" information available for 2O1E)

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:266
 aligned with ZNUA_BACSU | O34966 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:282
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315  
           ZNUA_BACSU    36 KLHVVTTFYPMYEFTKQIVKDKGDVDLLIPSSVEPHDWEPTPKDIANIQDADLFVYNSEYMETWVPSAEKSMGQGHAVFVNASKGIDLMEGSEEEHEEHDHGEHEHSHAMDPHVWLSPVLAQKEVKNITAQIVKQDPDNKEYYEKNSKEYIAKLQDLDKLYRTTAKKAEKKEFITQHTAFGYLAKEYGLKQVPIAGLSPDQEPSAASLAKLKTYAKEHNVKVIYFEEIASSKVADTLASEIGAKTEVLNTLEGLSKEEQDKGLGYIDIMKQNLDALKDSLLV 317
               SCOP domains d2o1ea_ A: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2o1eA01 A:16-183 Nitrogenase molybdenum iron protein domain                                                                                                             2o1eA02 A:184-297 Nitrogenase molybdenum iron protein domain                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhh..eeeee.............hhhhhhhhhhh.eeee.......hhhhhhhh......eeee..........----------------.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh..eeee..........hhhhhhhhhhhh......eee.....hhhhhhhhhhh...eee........hhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o1e A  16 KLHVVTTFYPmYEFTKQIVKDKGDVDLLIPSSVEPHDWEPTPKDIANIQDADLFVYNSEYmETWVPSAEKSmGQGHAVFVNASKGIDLmEG----------------HAmDPHVWLSPVLAQKEVKNITAQIVKQDPDNKEYYEKNSKEYIAKLQDLDKLYRTTAKKAEKKEFITQHTAFGYLAKEYGLKQVPIAGLSPDQEPSAASLAKLKTYAKEHNVKVIYFEEIASSKVADTLASEIGAKTEVLNTLEGLSKEEQDKGLGYIDImKQNLDALKDSLLV 297
                                    25|       35        45        55        65        75|       85 |      95       105|        -       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295  
                                     26-MSE                                            76-MSE     87-MSE          104-MSE            123 |                                                                                                                                                            284-MSE         
                                                                                                                    106                125-MSE

Chain B from PDB  Type:PROTEIN  Length:264
 aligned with ZNUA_BACSU | O34966 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:281
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315 
           ZNUA_BACSU    36 KLHVVTTFYPMYEFTKQIVKDKGDVDLLIPSSVEPHDWEPTPKDIANIQDADLFVYNSEYMETWVPSAEKSMGQGHAVFVNASKGIDLMEGSEEEHEEHDHGEHEHSHAMDPHVWLSPVLAQKEVKNITAQIVKQDPDNKEYYEKNSKEYIAKLQDLDKLYRTTAKKAEKKEFITQHTAFGYLAKEYGLKQVPIAGLSPDQEPSAASLAKLKTYAKEHNVKVIYFEEIASSKVADTLASEIGAKTEVLNTLEGLSKEEQDKGLGYIDIMKQNLDALKDSLL 316
               SCOP domains d2o1eb_ B: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2o1eB01 B:16-183 Nitrogenase molybdenum iron protein domain                                                                                                             2o1eB02 B:184-296 Nitrogenase molybdenum iron protein domain                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhh..eeeee.............hhhhhhhhhhh.eeee.......hhhhhhhh......eeee..........-----------------....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhh...eee..........hhhhhhhhhhhhhhh...eee.....hhhhhhhhh.....eee........hhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o1e B  16 KLHVVTTFYPmYEFTKQIVKDKGDVDLLIPSSVEPHDWEPTPKDIANIQDADLFVYNSEYmETWVPSAEKSmGQGHAVFVNASKGIDLmEG-----------------AmDPHVWLSPVLAQKEVKNITAQIVKQDPDNKEYYEKNSKEYIAKLQDLDKLYRTTAKKAEKKEFITQHTAFGYLAKEYGLKQVPIAGLSPDQEPSAASLAKLKTYAKEHNVKVIYFEEIASSKVADTLASEIGAKTEVLNTLEGLSKEEQDKGLGYIDImKQNLDALKDSLL 296
                                    25|       35        45        55        65        75|       85 |      95       105|        -       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
                                     26-MSE                                            76-MSE     87-MSE          104-MSE             124|                                                                                                                                                            284-MSE        
                                                                                                                    106                125-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Chelatase-like (149)

Superfamily: Helical backbone metal receptor (102)

Family: automated matches (30)

Protein domain: automated matches (30)

Bacillus subtilis [TaxId: 1423] (1)

1a	d2o1ea_	A:
1b	d2o1eb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Nitrogenase molybdenum iron protein domain (45)

Bacillus subtilis. Organism_taxid: 1423. Strain: 168. (2)

1a	2o1eB01	B:16-183
1b	2o1eA01	A:16-183
1c	2o1eA02	A:184-297
1d	2o1eB02	B:184-296

(no "Pfam Domain" information available for 2O1E)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ZNUA_BACSU | O34966)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0030001	metal ion transport	The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0010043	response to zinc ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0006829	zinc II ion transport	The directed movement of zinc (Zn II) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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