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- PDB-1dpp: DIPEPTIDE BINDING PROTEIN COMPLEX WITH GLYCYL-L-LEUCINE -

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Basic information

Entry
Database: PDB / ID: 1dpp
TitleDIPEPTIDE BINDING PROTEIN COMPLEX WITH GLYCYL-L-LEUCINE
ComponentsDIPEPTIDE BINDING PROTEIN
KeywordsPEPTIDE BINDING PROTEIN / CHEMOTAXIS / COMPLEX (BINDING PROTEIN-PEPTIDE) COMPLEX
Function / homology
Function and homology information


dipeptide transport / heme transport / dipeptide transmembrane transporter activity / heme transmembrane transport / peptide transmembrane transporter activity / positive chemotaxis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / : / peptide binding / protein transport ...dipeptide transport / heme transport / dipeptide transmembrane transporter activity / heme transmembrane transport / peptide transmembrane transporter activity / positive chemotaxis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / : / peptide binding / protein transport / outer membrane-bounded periplasmic space / heme binding / membrane
Similarity search - Function
: / Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 ...: / Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / LEUCINE / Dipeptide-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsDunten, P. / Mowbray, S.L.
CitationJournal: Protein Sci. / Year: 1995
Title: Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis.
Authors: Dunten, P. / Mowbray, S.L.
History
DepositionAug 11, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPEPTIDE BINDING PROTEIN
C: DIPEPTIDE BINDING PROTEIN
E: DIPEPTIDE BINDING PROTEIN
G: DIPEPTIDE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,72812
Polymers229,9034
Non-polymers8258
Water00
1
A: DIPEPTIDE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6823
Polymers57,4761
Non-polymers2062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DIPEPTIDE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6823
Polymers57,4761
Non-polymers2062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DIPEPTIDE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6823
Polymers57,4761
Non-polymers2062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: DIPEPTIDE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6823
Polymers57,4761
Non-polymers2062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.570, 182.570, 211.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: CIS PROLINE - PRO A 275 / 2: CIS PROLINE - PRO C 275 / 3: CIS PROLINE - PRO E 275 / 4: CIS PROLINE - PRO G 275
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.150197, 0.307245, -0.939703), (0.274181, -0.900258, -0.338172), (-0.949877, -0.308441, 0.050975)5.8578, 274.5383, 89.4968
2given(0.167259, -0.40796, 0.897548), (0.261819, -0.859306, -0.439368), (0.950513, 0.308484, -0.036915)7.4154, 264.54471, 7.2854
3given(-0.994153, 0.107633, 0.00871), (0.10759, 0.994181, -0.005285), (-0.009228, -0.004317, -0.999948)-17.5245, -8.5036, 97.9755

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Components

#1: Protein
DIPEPTIDE BINDING PROTEIN


Mass: 57475.863 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P23847
#2: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical
ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO2
Has protein modificationY
Nonpolymer detailsRESIDUES 1001 AND 1002 WITH CHAIN IDS A, C, E AND G FORM THE DIPEPTIDE SUBSTRATE BOUND TO THE ...RESIDUES 1001 AND 1002 WITH CHAIN IDS A, C, E AND G FORM THE DIPEPTIDE SUBSTRATE BOUND TO THE DIPEPTIDE-BINDING PROTEIN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.42 Å3/Da / Density % sol: 72.15 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein 1drop
21 mMdepeptide1drop
31.49 Msodium citrate1reservoir
41 %ethanol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.89
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 17, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 57483 / % possible obs: 88 % / Redundancy: 3 % / Rmerge(I) obs: 0.105
Reflection
*PLUS
Num. measured all: 170663 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.28 Å / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
RefinementResolution: 3.2→25 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.24 -5 %
Rwork0.223 --
obs0.223 57347 87 %
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16192 0 52 0 16244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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