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- PDB-2d5w: The crystal structure of oligopeptide binding protein from Thermu... -

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Basic information

Entry
Database: PDB / ID: 2d5w
TitleThe crystal structure of oligopeptide binding protein from Thermus thermophilus HB8 complexed with pentapeptide
Components
  • pentapeptide A
  • pentapeptide B
  • peptide ABC transporter, peptide-binding protein
KeywordsPEPTIDE BINDING PROTEIN / PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / 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 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / 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
Peptide ABC transporter, peptide-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsMorita, A.
CitationJournal: To be Published
Title: The crystal structure of oligopeptide binding protein from Thermus thermophilus HB8 complexed with pentapeptide
Authors: Morita, A. / Sakai, N. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionNov 7, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptide ABC transporter, peptide-binding protein
B: peptide ABC transporter, peptide-binding protein
C: pentapeptide A
D: pentapeptide B


Theoretical massNumber of molelcules
Total (without water)138,4774
Polymers138,4774
Non-polymers00
Water19,2761070
1
A: peptide ABC transporter, peptide-binding protein
C: pentapeptide A


Theoretical massNumber of molelcules
Total (without water)69,2372
Polymers69,2372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-4 kcal/mol
Surface area22270 Å2
MethodPISA
2
B: peptide ABC transporter, peptide-binding protein
D: pentapeptide B


Theoretical massNumber of molelcules
Total (without water)69,2402
Polymers69,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-2 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.600, 109.200, 114.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein peptide ABC transporter, peptide-binding protein / Oligopeptide binding protein


Mass: 68704.859 Da / Num. of mol.: 2 / Fragment: residues 1-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1634 / Plasmid: pET-26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHU6
#2: Protein/peptide pentapeptide A


Mass: 531.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8
Description: This peptide was co-purified and co-crystallized with the protein.
Gene: TTHA1634 / Plasmid: pET-26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Protein/peptide pentapeptide B


Mass: 535.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8
Description: This peptide was co-purified and co-crystallized with the protein.
Gene: TTHA1634 / Plasmid: pET-26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1070 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.15M lithium nitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44B210.900, 0.9788, 0.9793
SYNCHROTRONSPring-8 BL41XU20.9
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDSep 30, 2004
ADSC QUANTUM 3152CCDOct 4, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97881
30.97931
ReflectionResolution: 1.25→50 Å / Num. obs: 346050 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 17.709 Å2 / Rsym value: 0.095 / Net I/σ(I): 31
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 6.3 / Rsym value: 0.412 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.3→15 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.196 30683 RANDOM
Rwork0.186 --
obs-307850 -
Displacement parametersBiso mean: 11.527 Å2
Baniso -1Baniso -2Baniso -3
1-0.865 Å20 Å20 Å2
2---1.385 Å20 Å2
3---0.521 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.1514 Å0.142 Å
Luzzati d res low-5 Å
Luzzati sigma a0.0777 Å0.0529 Å
Refinement stepCycle: LAST / Resolution: 1.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9772 0 0 1070 10842
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.30292
X-RAY DIFFRACTIONc_bond_d0.004557
X-RAY DIFFRACTIONc_dihedral_angle_d23.82132
X-RAY DIFFRACTIONc_improper_angle_d0.84721
LS refinement shellResolution: 1.3→1.35 Å
Rfactor% reflection
Rfree0.2302 -
Rwork0.2119 -
obs-0.1014 %

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