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

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Basic information

Entry
Database: PDB / ID: 4qfk
TitleCrystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913
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
Periplasmic dipeptide-binding protein
Similarity search - Component
Biological speciesPseudoalteromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.288 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 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
H: ABC transporter periplasmic peptide-binding protein
A: ABC transporter periplasmic peptide-binding protein
B: ABC transporter periplasmic peptide-binding protein
C: ABC transporter periplasmic peptide-binding protein
D: ABC transporter periplasmic peptide-binding protein
E: ABC transporter periplasmic peptide-binding protein
F: ABC transporter periplasmic peptide-binding protein
G: ABC transporter periplasmic peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)494,1038
Polymers494,1038
Non-polymers00
Water30,3011682
1
H: ABC transporter periplasmic peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)61,7631
Polymers61,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: ABC transporter periplasmic peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)61,7631
Polymers61,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: ABC transporter periplasmic peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)61,7631
Polymers61,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: ABC transporter periplasmic peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)61,7631
Polymers61,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: ABC transporter periplasmic peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)61,7631
Polymers61,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: ABC transporter periplasmic peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)61,7631
Polymers61,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: ABC transporter periplasmic peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)61,7631
Polymers61,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
G: ABC transporter periplasmic peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)61,7631
Polymers61,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.386, 93.970, 140.549
Angle α, β, γ (deg.)80.03, 84.43, 69.84
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 61762.934 Da / Num. of mol.: 8
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1682 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 9.2
Details: 0.2M potassium phosphate dibasic, 20%(w/v) polyethylene glycol 3350, pH 9.2, EVAPORATION, temperature 277K

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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: Nov 1, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.288→50 Å / Num. all: 185390 / Num. obs: 185390 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.8 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 93.6

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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: 1dpe

1dpe


Resolution: 2.288→42.629 Å / FOM work R set: 0.7975 / SU ML: 0.33 / σ(F): 0.02 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 8883 5.03 %
Rwork0.1913 --
obs0.1946 176680 88.69 %
all-185390 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.525 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 104.81 Å2 / Biso mean: 29.32 Å2 / Biso min: 6.91 Å2
Baniso -1Baniso -2Baniso -3
1-5.3673 Å2-2.9062 Å2-0.0214 Å2
2---6.8966 Å2-2.5764 Å2
3---1.5293 Å2
Refinement stepCycle: LAST / Resolution: 2.288→42.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32488 0 0 1682 34170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833344
X-RAY DIFFRACTIONf_angle_d1.18345336
X-RAY DIFFRACTIONf_chiral_restr0.084960
X-RAY DIFFRACTIONf_plane_restr0.0065888
X-RAY DIFFRACTIONf_dihedral_angle_d16.76212160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.288-2.3140.288820.23971942202431
2.314-2.34120.34162980.24145217551582
2.3412-2.36970.32072670.22415287555484
2.3697-2.39970.32682400.22955389562985
2.3997-2.43130.32053190.23265291561085
2.4313-2.46460.34032830.23535373565685
2.4646-2.49980.33112710.22965399567086
2.4998-2.53710.3232890.20985507579687
2.5371-2.57680.31142920.22165407569987
2.5768-2.6190.30823080.23315526583487
2.619-2.66420.33482840.22965535581988
2.6642-2.71260.30752580.22795615587388
2.7126-2.76480.31593250.2265644596989
2.7648-2.82120.30622970.22525699599690
2.8212-2.88250.28973150.2315714602991
2.8825-2.94960.31213240.22315752607692
2.9496-3.02330.29383300.21025777610792
3.0233-3.1050.2813140.21855868618293
3.105-3.19640.27812930.20955971626494
3.1964-3.29950.28133230.20255939626295
3.2995-3.41740.25283180.20035972629094
3.4174-3.55410.23542990.18985981628095
3.5541-3.71580.22873440.17866054639896
3.7158-3.91160.21323070.15765938624595
3.9116-4.15650.19122990.14095994629395
4.1565-4.47710.1913080.14536013632195
4.4771-4.9270.19543410.14595921626294
4.927-5.63860.21943070.16065992629995
5.6386-7.09870.21673270.17166101642897
7.0987-42.63620.22833210.1795979630095

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