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- PDB-5f1q: Crystal Structure of Periplasmic Dipeptide Transport Protein from... -

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Basic information

Entry
Database: PDB / ID: 5f1q
TitleCrystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis
ComponentsPeriplasmic dipeptide transport protein
KeywordsHYDROLASE / alpha-beta fold / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / 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 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / DI(HYDROXYETHYL)ETHER / Periplasmic dipeptide transport protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.956 Å
AuthorsKim, Y. / Zhou, M. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis
Authors: Kim, Y. / Zhou, M. / Shatsman, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic dipeptide transport protein
B: Periplasmic dipeptide transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,89623
Polymers124,2352
Non-polymers1,66121
Water8,683482
1
A: Periplasmic dipeptide transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,95411
Polymers62,1181
Non-polymers83610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic dipeptide transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,94212
Polymers62,1181
Non-polymers82411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)289.290, 59.745, 80.631
Angle α, β, γ (deg.)90.00, 103.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-707-

HOH

21B-894-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Periplasmic dipeptide transport protein


Mass: 62117.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: Nepal516 / Gene: YPN_3652 / Plasmid: pMCSG28 / Details (production host): C-terminal His6 tag / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2YM47

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Non-polymers , 6 types, 503 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M phosphate-citrate, pH 4.2, 40:5(v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 93243 / Num. obs: 93243 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 22.04 Å2 / Rsym value: 0.152 / Net I/σ(I): 7.98
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.42 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection
RefinementResolution: 1.956→28.311 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 4439 5.03 %random
Rwork0.1656 ---
obs0.1674 88295 91.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.4 Å2
Refinement stepCycle: LAST / Resolution: 1.956→28.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8142 0 105 482 8729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098583
X-RAY DIFFRACTIONf_angle_d1.13111622
X-RAY DIFFRACTIONf_dihedral_angle_d15.0483239
X-RAY DIFFRACTIONf_chiral_restr0.0471203
X-RAY DIFFRACTIONf_plane_restr0.0061534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.956-1.97840.233890.2648246X-RAY DIFFRACTION8
1.9784-2.00170.2677750.24161441X-RAY DIFFRACTION47
2.0017-2.02610.29571210.22622342X-RAY DIFFRACTION78
2.0261-2.05170.25061330.20672644X-RAY DIFFRACTION86
2.0517-2.07870.23751340.20282709X-RAY DIFFRACTION89
2.0787-2.10710.22711350.19552764X-RAY DIFFRACTION91
2.1071-2.13720.23951350.18332880X-RAY DIFFRACTION93
2.1372-2.16910.20971330.18032866X-RAY DIFFRACTION95
2.1691-2.2030.23861680.18022911X-RAY DIFFRACTION96
2.203-2.23910.20241510.18062946X-RAY DIFFRACTION96
2.2391-2.27770.23541470.17622931X-RAY DIFFRACTION96
2.2777-2.31910.22151420.17112908X-RAY DIFFRACTION96
2.3191-2.36370.22021580.16972964X-RAY DIFFRACTION96
2.3637-2.41190.19551650.17122900X-RAY DIFFRACTION97
2.4119-2.46430.2241690.17112974X-RAY DIFFRACTION97
2.4643-2.52160.17621590.16752952X-RAY DIFFRACTION97
2.5216-2.58460.22891660.17392971X-RAY DIFFRACTION97
2.5846-2.65450.20541810.17312936X-RAY DIFFRACTION97
2.6545-2.73250.20421460.1763023X-RAY DIFFRACTION98
2.7325-2.82060.21891670.18192971X-RAY DIFFRACTION98
2.8206-2.92140.20531460.183030X-RAY DIFFRACTION99
2.9214-3.03820.21161850.17283048X-RAY DIFFRACTION99
3.0382-3.17630.21831840.17883016X-RAY DIFFRACTION100
3.1763-3.34350.19561630.17253097X-RAY DIFFRACTION99
3.3435-3.55260.18761380.16043058X-RAY DIFFRACTION99
3.5526-3.82630.18361710.15213054X-RAY DIFFRACTION99
3.8263-4.21030.17851480.13783061X-RAY DIFFRACTION99
4.2103-4.81690.16911580.13193054X-RAY DIFFRACTION99
4.8169-6.0590.17721740.14453089X-RAY DIFFRACTION99
6.059-28.31440.16831780.15533070X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.55620.4679-0.63951.1233-0.24581.32760.0662-0.10760.18950.12470.01570.1459-0.0999-0.1821-0.05170.10150.0040.00770.14720.00360.142147.2727-22.257812.6221
20.83570.24760.14740.78710.12440.60470.04940.0286-0.1799-0.01290.0088-0.00580.1497-0.0404-0.05440.1040.0026-0.01750.09330.00140.143851.6715-42.89650.6342
31.71270.0297-0.34191.27230.0331.3563-0.01730.08190.2029-0.31680.0767-0.184-0.24680.1937-0.05610.2931-0.05820.04810.1935-0.03640.172435.4135-21.1073-38.0769
40.7576-0.06050.35421.1402-0.25881.33020.0655-0.0912-0.0692-0.03020.04610.12920.0615-0.2127-0.11160.1171-0.0328-0.02980.1962-0.0160.137620.4232-38.9711-20.7377
51.1904-0.03380.47111.4152-0.09183.48070.11160.1917-0.1115-0.39630.06640.0220.19990.2981-0.11660.25540.0105-0.02710.1799-0.06350.187832.2954-46.7724-35.6743
60.79550.34050.31180.7398-0.09781.62570.02210.0497-0.008-0.18870.08040.2036-0.0505-0.178-0.0360.16290.0036-0.04150.1891-0.01830.13217.759-31.7664-34.0267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:288 )A29 - 288
2X-RAY DIFFRACTION2( CHAIN A AND RESID 289:541 )A289 - 541
3X-RAY DIFFRACTION3( CHAIN B AND RESID 29:258 )B29 - 258
4X-RAY DIFFRACTION4( CHAIN B AND RESID 259:448 )B259 - 448
5X-RAY DIFFRACTION5( CHAIN B AND RESID 449:479 )B449 - 479
6X-RAY DIFFRACTION6( CHAIN B AND RESID 480:535 )B480 - 535

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