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Title :   CRYSTAL STRUCTURE OF DING PROTEIN

Authors :   Z. Q. Gai, A. Nakamura, Y. Tanaka, N. Hirano, I. Tanaka, M. Yao

Date :   17 Apr 13 (Deposition) - 30 Oct 13 (Release) - 30 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

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

Keywords :   Phosphate Binding Protein, Phosphate, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Q. Gai, A. Nakamura, Y. Tanaka, N. Hirano, I. Tanaka, M. Yao
Crystal Structure Analysis, Overexpression And Refolding Behaviour Of A Ding Protein With Single Mutation.
J. Synchrotron Radiat. V. 20 854 2013
PubMed-ID: 24121327 | Reference-DOI: 10.1107/S0909049513020694

Molecule 1 - DING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	UNIDENTIFIED PROKARYOTIC ORGANISM
	Organism Taxid	:	2725
	Synonym	:	HPBP

		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, 10)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:7 , THR A:8 , LEU A:9 , GLY A:31 , SER A:32 , ASP A:61 , ARG A:140 , SER A:144 , GLY A:145 , THR A:146	BINDING SITE FOR RESIDUE PO4 A 401
02	AC2	SOFTWARE	LYS A:110 , ARG A:119 , THR A:160 , HOH A:694 , HOH A:802 , ALA B:348 , ARG B:351 , ALA B:352 , THR B:356 , HOH B:502	BINDING SITE FOR RESIDUE GOL A 402
03	AC3	SOFTWARE	LEU A:179 , LEU A:182 , GLY A:184 , ALA A:185 , HOH A:666 , HOH A:982 , HOH A:1000 , ALA B:188 , THR B:189	BINDING SITE FOR RESIDUE GOL A 403
04	AC4	SOFTWARE	ASP A:1 , THR A:311 , GLN A:312 , GLN A:376 , HOH A:597 , HOH A:763 , HOH A:765 , HOH A:952 , HOH A:1096	BINDING SITE FOR RESIDUE GOL A 404
05	AC5	SOFTWARE	PHE A:97 , ARG A:98 , LEU A:198 , ASN A:199 , LYS A:228 , HOH A:719	BINDING SITE FOR RESIDUE GOL A 405
06	AC6	SOFTWARE	ALA B:7 , THR B:8 , LEU B:9 , GLY B:31 , SER B:32 , ASP B:61 , ARG B:140 , SER B:144 , GLY B:145 , THR B:146	BINDING SITE FOR RESIDUE PO4 B 401
07	AC7	SOFTWARE	ALA A:188 , THR A:189 , LEU B:179 , LEU B:182 , GLY B:184 , ALA B:185 , HOH B:528 , HOH B:613 , HOH B:953	BINDING SITE FOR RESIDUE GOL B 402
08	AC8	SOFTWARE	PRO B:260 , PRO B:262 , VAL B:272 , PRO B:275 , GLY B:284 , HOH B:513	BINDING SITE FOR RESIDUE GOL B 403
09	AC9	SOFTWARE	PHE B:97 , ARG B:98 , ASN B:199 , LYS B:228 , HOH B:675 , HOH B:802	BINDING SITE FOR RESIDUE GOL B 404
10	BC1	SOFTWARE	ASP B:1 , THR B:311 , GLN B:312 , HOH B:523 , HOH B:633 , HOH B:1016	BINDING SITE FOR RESIDUE GOL B 405

Asymmetric Unit

No.	Residues
1	A:113	-	A:158
2	A:306	-	A:369
3	B:113	-	B:158
4	B:306	-	B:369

(no "Cis Peptide Bond" information available for 3W9W)

(no "SAP(SNP)/Variant" information available for 3W9W)

(no "PROSITE Motif" information available for 3W9W)

(no "Exon" information available for 3W9W)

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:376
 aligned with PHBP_UNKP | P85173 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:376
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370      
            PHBP_UNKP     1 DINGGGATLPQKLYLTPDVLTAGFAPYIGVGSGKGKIAFLENKYNQFGTDTTKNVHWAGSDSKLTATELATYAADKEPGWGKLIQVPSVATSVAIPFRKAGANAVDLSVKELCGVFSGRIADWSGITGAGRSGPIQVVYRAESSGTTELFTRFLNAKCTTEPGTFAVTTTFANSYSLGLTPLAGAVAATGSDGVMAALNDTTVAEGRITYISPDFAAPTLAGLDDATKVARVGKGVVNGVAVEGKSPAAANVSAAISVVPLPAAADRGNPDVWVPVFGATTGGGVVAYPDSGYPILGFTNLIFSQCYANATQTGQVRDFFTKHYGTSANNDAAIEANAFVPLPSNWKAAVRASFLTASNALSIGNTNVCNGKGRPQ 376
               SCOP domains d3w9wa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...hhhhhh............ee.hhhhhhhhhhhhhhhhh.........eeee....hhhhhhhhhhhhhhhhh.eeeeeeeeee.............eehhhhhhhhhhh...hhhhh.........eeeee...hhhhhhhhhhhhhhh...........hhhhh...........eeehhhhhhhhhhh.......ee...hhhhhh..hhhhhh.....ee..eee..eee.....hhhhhhhhhhh....hhhhh.hhhhhh..ee.......ee........eeeeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhhhhh.........hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w9w A   1 DINGGGATLPQKLYLTPDVLTAGFAPYIGVGSGKGKIAFLENKYNQFGTDTTKNVHWAGSDSKLTATELATYAADKEPGWGKLIQVPSVATSVAIPFRKAGANAVDLSVKELCGVFSGRIADWSGITGAGRSGPIQVVYRAESSGTTELFTRFLNAKCTTEPGTFAVTTTFANSYSLGLTPLAGAVAATGSDGVMAALNDTTVAEGRITYMSPDFAAPTLAGLDDATKVARVGKGVVNGVAVEGKSPAAANVSAAISVVPLPAAADRGNPDVWVPVFGATTGGGVVAYPDSGYPILGFTNLIFSQCYANATQTGQVRDFFTKHYGTSANNDAAIEANAFVPLPSNWKAAVRASFLTASNALSIGNTNVCNGKGRPQ 376
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370

Chain B from PDB  Type:PROTEIN  Length:376
 aligned with PHBP_UNKP | P85173 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:376
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370      
            PHBP_UNKP     1 DINGGGATLPQKLYLTPDVLTAGFAPYIGVGSGKGKIAFLENKYNQFGTDTTKNVHWAGSDSKLTATELATYAADKEPGWGKLIQVPSVATSVAIPFRKAGANAVDLSVKELCGVFSGRIADWSGITGAGRSGPIQVVYRAESSGTTELFTRFLNAKCTTEPGTFAVTTTFANSYSLGLTPLAGAVAATGSDGVMAALNDTTVAEGRITYISPDFAAPTLAGLDDATKVARVGKGVVNGVAVEGKSPAAANVSAAISVVPLPAAADRGNPDVWVPVFGATTGGGVVAYPDSGYPILGFTNLIFSQCYANATQTGQVRDFFTKHYGTSANNDAAIEANAFVPLPSNWKAAVRASFLTASNALSIGNTNVCNGKGRPQ 376
               SCOP domains d3w9wb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...hhhhhh............ee.hhhhhhhhhhhhhhhhh.........eeee....hhhhhhhhhhhhhhhhh.eeeeeeeeee.............eehhhhhhhhhhh...hhhhh.........eeeee...hhhhhhhhhhhhhhh...........hhhhh...........eeehhhhhhhhhhh.......ee...........hhhhhh.....ee..eee..eee.....hhhhhhhhhhh..........hhhhhh..ee.......ee........eeeeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w9w B   1 DINGGGATLPQKLYLTPDVLTAGFAPYIGVGSGKGKIAFLENKYNQFGTDTTKNVHWAGSDSKLTATELATYAADKEPGWGKLIQVPSVATSVAIPFRKAGANAVDLSVKELCGVFSGRIADWSGITGAGRSGPIQVVYRAESSGTTELFTRFLNAKCTTEPGTFAVTTTFANSYSLGLTPLAGAVAATGSDGVMAALNDTTVAEGRITYMSPDFAAPTLAGLDDATKVARVGKGVVNGVAVEGKSPAAANVSAAISVVPLPAAADRGNPDVWVPVFGATTGGGVVAYPDSGYPILGFTNLIFSQCYANATQTGQVRDFFTKHYGTSANNDAAIEANAFVPLPSNWKAAVRASFLTASNALSIGNTNVCNGKGRPQ 376
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: automated matches (76)

Unidentified prokaryotic [TaxId: 2725] (3)

1a	d3w9wa_	A:
1b	d3w9wb_	B:

(no "CATH Domain" information available for 3W9W)

(no "Pfam Domain" information available for 3W9W)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PHBP_UNKP | P85173)

biological process
	GO:0006817	phosphate ion transport	The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3w9w)

Biological Units
	Complete Structure
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Access by PDB/NDB ID
	3w9w
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	PHBP_UNKP \| P85173
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	PHBP_UNKP \| P85173
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UniProtKB/Swiss-Prot
	PHBP_UNKP \| P85173	:	2v3q 3w9v 4m1v

2q9t	THE SAME PROTEIN FROM PSEUDOMONAS FLUORESCENS
2v3q	THE SAME PROTEIN FROM HUMAN
3g62	THE SAME PROTEIN FROM PSEUDOMONAS FLUORESCENS
3w9v

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (3, 3)

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Related Entries Specified in the PDB File