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

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Basic information

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


ATP-binding cassette (ABC) transporter complex / transmembrane transport / 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
PHOSPHATE ION / THREONINE / VALINE / Periplasmic dipeptide-binding protein
Similarity search - Component
Biological speciesPseudoalteromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 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

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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)124,37310
Polymers123,5262
Non-polymers8478
Water14,520806
1
A: ABC transporter periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0944
Polymers61,7631
Non-polymers3313
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)62,2786
Polymers61,7631
Non-polymers5155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.949, 105.949, 101.263
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 814 molecules

#2: Chemical ChemComp-VAL / VALINE / Valine


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-THR / THREONINE / Threonine


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H2O

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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: 53.7 %
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
Reflection twinOperator: h,-h-k,-l / Fraction: 0.279
ReflectionResolution: 1.9→50 Å / Num. all: 98926 / Num. obs: 98926 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.66 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 98.8

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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: 1.903→34.68 Å / FOM work R set: 0.841 / σ(F): 0 / Phase error: 24.02 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1773 4943 5 %
Rwork0.1546 93924 -
obs0.1562 98919 99.23 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.429 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 69.83 Å2 / Biso mean: 23.58 Å2 / Biso min: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.4458 Å2-0 Å2-0 Å2
2--1.4458 Å20 Å2
3----2.8916 Å2
Refinement stepCycle: LAST / Resolution: 1.903→34.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8160 0 52 806 9018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068516
X-RAY DIFFRACTIONf_angle_d0.97111590
X-RAY DIFFRACTIONf_chiral_restr0.0691265
X-RAY DIFFRACTIONf_plane_restr0.0051508
X-RAY DIFFRACTIONf_dihedral_angle_d14.5033110
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 (%)
1.9035-1.93630.36912610.30834644490593
1.9363-1.97150.30272400.28124667490794
1.9715-2.00940.26352230.2544738496194
2.0094-2.05040.26722400.23714637487794
2.0504-2.0950.26162710.2194700497194
2.095-2.14370.24752560.20914629488594
2.1437-2.19730.21632490.19794696494594
2.1973-2.25670.21422510.18554761501294
2.2567-2.32310.19892420.1784683492595
2.3231-2.39810.21262270.17264714494195
2.3981-2.48370.19642240.16714763498795
2.4837-2.58310.19612510.16734707495895
2.5831-2.70060.19042340.16474696493095
2.7006-2.84290.17242470.15664674492194
2.8429-3.02080.1562480.14754713496194
3.0208-3.25380.16922540.13974745499994
3.2538-3.58070.13352710.11874656492794
3.5807-4.09760.11952530.10394671492494
4.0976-5.1580.11662540.09724713496795
5.158-29.2820.15332360.13484717495394

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