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

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Basic information

Entry
Database: PDB / ID: 4qfl
TitleCrystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 in complex with Ala-Phe
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
ALANINE / PHENYLALANINE / Periplasmic dipeptide-binding protein
Similarity search - Component
Biological speciesPseudoalteromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 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)124,2198
Polymers123,5262
Non-polymers6936
Water12,358686
1
A: ABC transporter periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1094
Polymers61,7631
Non-polymers3463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1094
Polymers61,7631
Non-polymers3463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.142, 106.142, 100.981
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-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#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.: 686 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
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: 1.749→50 Å / Num. all: 126524 / Num. obs: 126524 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2
Reflection shellResolution: 1.75→1.81 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: 1dpp

1dpp


Resolution: 1.749→33.988 Å / FOM work R set: 0.7761 / σ(F): 0 / Phase error: 30.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1836 6441 5.09 %
Rwork0.1603 --
obs0.1617 126489 98.36 %
all-126524 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.217 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 64.47 Å2 / Biso mean: 24.45 Å2 / Biso min: 12.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.0965 Å2-0 Å2-0 Å2
2--1.0965 Å20 Å2
3----2.193 Å2
Refinement stepCycle: LAST / Resolution: 1.749→33.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8160 0 46 686 8892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078480
X-RAY DIFFRACTIONf_angle_d1.01211534
X-RAY DIFFRACTIONf_chiral_restr0.071257
X-RAY DIFFRACTIONf_plane_restr0.0041502
X-RAY DIFFRACTIONf_dihedral_angle_d14.4253096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.749-1.77920.353400.32376099643995
1.7792-1.81150.30133680.28466103647194
1.8115-1.84630.30213150.25636033634895
1.8463-1.8840.26393370.23836129646695
1.884-1.9250.22093160.22176137645395
1.925-1.96970.23673070.21126072637995
1.9697-2.01890.2212810.20536185646696
2.0189-2.07350.20723110.19596064637595
2.0735-2.13440.20313530.19446078643194
2.1344-2.20320.22712920.17916103639595
2.2032-2.28190.17473030.18046114641795
2.2819-2.37310.19533360.17446033636994
2.3731-2.4810.17643260.17346056638294
2.481-2.61160.19283160.1756006632294
2.6116-2.77490.18432930.16626055634894
2.7749-2.98860.18523230.15695980630393
2.9886-3.28830.18083110.14785894620592
3.2883-3.76180.16623000.12535776607690
3.7618-4.73060.13853100.10085657596788
4.7306-21.08980.14533100.12445518582886

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