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- PDB-4qfo: Crystal structure of dipeptide binding protein from pseudoalterom... -

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Basic information

Entry
Database: PDB / ID: 4qfo
TitleCrystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 in complex with Met-Leu
ComponentsABC transporter periplasmic peptide-binding protein
KeywordsPEPTIDE BINDING PROTEIN / dipeptide binding protein
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
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 / Bacterial extracellular solute-binding proteins, family 5 Middle ...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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LEUCINE / METHIONINE / Periplasmic dipeptide-binding protein
Similarity search - Component
Biological speciesPseudoalteromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsLi, C.Y. / Zhang, Y.Z.
CitationJournal: J. Bacteriol. / Year: 2015
Title: Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913
Authors: Li, C.Y. / Chen, X.L. / Qin, Q.L. / Wang, P. / Zhang, W.X. / Xie, B.B. / Su, H.N. / Zhang, X.Y. / Zhou, B.C. / Zhang, Y.Z.
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter periplasmic peptide-binding protein
B: ABC transporter periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2718
Polymers123,5262
Non-polymers7456
Water7,800433
1
A: ABC transporter periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1354
Polymers61,7631
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1354
Polymers61,7631
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-11 kcal/mol
Surface area36810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.403, 100.403, 106.931
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein ABC transporter periplasmic peptide-binding protein / Periplasmic dipeptide-binding protein


Mass: 61762.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas (bacteria) / Strain: SM9913 / Gene: dppA / Production host: Escherichia coli (E. coli) / References: UniProt: A7Y7W1
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.5M sodium phosphate monobasic monohydrate, 0.9M potassium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 53350 / Num. obs: 53350 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.48 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QFL

4qfl


Resolution: 2.304→33.731 Å / FOM work R set: 0.8589 / SU ML: 0.24 / σ(F): 0.09 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 2583 5.07 %
Rwork0.1599 --
obs0.1625 50905 95.44 %
all-53350 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.331 Å2 / ksol: 0.439 e/Å3
Displacement parametersBiso max: 88.61 Å2 / Biso mean: 28.78 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.1053 Å2-0 Å20 Å2
2---0.1053 Å2-0 Å2
3---0.2107 Å2
Refinement stepCycle: LAST / Resolution: 2.304→33.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8160 0 46 433 8639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088517
X-RAY DIFFRACTIONf_angle_d1.11711582
X-RAY DIFFRACTIONf_chiral_restr0.0811261
X-RAY DIFFRACTIONf_plane_restr0.0051506
X-RAY DIFFRACTIONf_dihedral_angle_d14.2813123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3038-2.34810.27141390.18962544268389
2.3481-2.3960.27291270.19182533266090
2.396-2.44810.25551200.17682598271891
2.4481-2.5050.24481330.17072537267091
2.505-2.56760.26321190.16432598271791
2.5676-2.6370.23971380.17312617275594
2.637-2.71460.24041410.17082699284095
2.7146-2.80220.24351440.16692641278595
2.8022-2.90230.26761200.17032687280796
2.9023-3.01840.21941430.16412708285196
3.0184-3.15570.21831390.15932772291198
3.1557-3.32190.19471670.15572717288498
3.3219-3.52990.19471630.14352735289898
3.5299-3.80210.19911370.1442790292799
3.8021-4.18410.16331660.12462785295199
4.1841-4.7880.15881390.122828122951100
4.788-6.02680.16921750.15872768294399
6.0268-33.73490.24211730.212727812954100

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