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- PDB-4gl8: X-ray crystal structure of a periplasmic oligopeptide-binding pro... -

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Basic information

Entry
Database: PDB / ID: 4gl8
TitleX-ray crystal structure of a periplasmic oligopeptide-binding protein/Oligopeptide ABC transporter(OppAIV) from Borrelia burgdorferi
Components
  • Oligopeptide ABC transporter OppAIV
  • Peptide of unknown sequence
KeywordsPROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ABC transporter / transporter / peptide binding / unknown peptide
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
Oligopeptide ABC transporter OppAIV
Similarity search - Component
Biological speciesBorrelia burgdorferi B31 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: X-ray crystal structure of a periplasmic oligopeptide-binding protein/Oligopeptide ABC transporter(OppAIV) from Borrelia burgdorferi
Authors: Fairman, J.W. / Abendroth, J. / Sankaran, B. / Staker, B.L.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oligopeptide ABC transporter OppAIV
B: Oligopeptide ABC transporter OppAIV
C: Peptide of unknown sequence
D: Peptide of unknown sequence


Theoretical massNumber of molelcules
Total (without water)121,9494
Polymers121,9494
Non-polymers00
Water8,305461
1
A: Oligopeptide ABC transporter OppAIV
C: Peptide of unknown sequence


Theoretical massNumber of molelcules
Total (without water)60,9752
Polymers60,9752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-4 kcal/mol
Surface area19700 Å2
MethodPISA
2
B: Oligopeptide ABC transporter OppAIV
D: Peptide of unknown sequence


Theoretical massNumber of molelcules
Total (without water)60,9752
Polymers60,9752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-4 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.750, 103.580, 104.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Oligopeptide ABC transporter OppAIV


Mass: 60616.293 Da / Num. of mol.: 2 / Fragment: UNP residues 24-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi B31 (bacteria) / Strain: B31 / Gene: oppAIV, BB_B16 / Production host: Escherichia coli (E. coli) / References: UniProt: H7C7K8
#2: Protein/peptide Peptide of unknown sequence


Mass: 358.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: protein purified bound to this peptide with unknown sequence
Source: (natural) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.12
Details: Morpheus G4: 1x MORPHEUS PRECIPITANTS, 1x MORPHEUS CARBOHYDRATES, 1x MORPHEUS BUFFER ph 6.12, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 55780 / Num. obs: 55023 / % possible obs: 98.643 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.78 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.74

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OLA

1ola


Resolution: 2.2→19.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.692 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22046 2800 5.1 %RANDOM
Rwork0.17175 ---
all0.17425 52943 --
obs0.17425 52223 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.594 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å2-0 Å2-0 Å2
2---0.96 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7965 0 0 461 8426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028167
X-RAY DIFFRACTIONr_bond_other_d0.0010.027592
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.96211097
X-RAY DIFFRACTIONr_angle_other_deg0.803317460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01951012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80524.869382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.115151375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7581538
X-RAY DIFFRACTIONr_chiral_restr0.0810.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021871
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 197 -
Rwork0.222 3382 -
obs--87.89 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.742-0.21780.56790.8917-0.07081.11020.00180.0402-0.0206-0.0209-0.017-0.01580.11660.09480.01520.03090.00080.00280.10270.00570.065999.58547.841115.816
22.1008-0.48141.30111.1698-0.06352.0752-0.00380.26040.0255-0.17020.00830.14350.06430.2898-0.00450.0601-0.033-0.01840.0995-0.00880.050185.964848.7352-2.3386
30.5340.29070.7992.84631.24911.4887-0.0389-0.0588-0.0153-0.0351-0.06960.3527-0.1154-0.12630.10850.06240.0212-0.01590.12310.0040.13278.502669.768512.9342
41.2063-0.34110.43082.35-0.34722.0462-0.0882-0.0977-0.19540.16870.20640.5120.03-0.3658-0.11820.0211-0.00890.04430.17460.03040.155673.85869.577422.4533
51.6008-1.0843-0.22592.41480.9061.5951-0.04920.0320.0094-0.19510.03160.0913-0.0938-0.03060.01760.0696-0.0162-0.03960.06990.04390.042683.461980.188511.085
60.5780.17770.15730.77030.11611.0664-0.0346-0.029-0.04620.05330.06640.136-0.04840.0086-0.03180.01830.00710.00160.08390.03520.082185.318360.422721.7328
70.832-0.40530.47930.97-0.28731.2857-0.05970.02050.01620.0653-0.0206-0.14080.05130.04820.08030.06080.02490.03050.07640.01550.060450.20237.334713.6186
80.1769-0.0201-0.01221.80340.3540.85480.0220.02090.036-0.118-0.01870.0259-0.039-0.0239-0.00330.0160.00070.01530.11130.01630.040331.57254.61253.3201
91.52031.2666-0.61394.813-0.19551.1994-0.01880.05990.07670.10390.03040.42-0.1477-0.0953-0.01150.04620.02840.01820.0772-0.00990.049328.004767.270517.903
100.4974-0.1107-0.06541.5182-0.33931.5163-0.05790.0330.0113-0.0354-0.0046-0.0535-0.02070.07870.06240.052-0.00980.01670.07880.00330.045538.995762.9749.648
110.2553-0.2095-0.20962.28090.17773.697-0.0322-0.09140.070.530.0227-0.03550.21170.12840.00950.16210.02710.00360.1134-0.01370.031336.880458.046528.718
122.0095-0.3671.17051.9141.23413.844-0.02340.1028-0.1035-0.063-0.08490.26880.1366-0.020.10830.0703-0.02610.01370.0961-0.00770.0730.077236.92252.5695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 203
2X-RAY DIFFRACTION2A204 - 265
3X-RAY DIFFRACTION3A266 - 311
4X-RAY DIFFRACTION4A312 - 353
5X-RAY DIFFRACTION5A354 - 427
6X-RAY DIFFRACTION6A428 - 529
7X-RAY DIFFRACTION7B31 - 234
8X-RAY DIFFRACTION8B235 - 319
9X-RAY DIFFRACTION9B320 - 372
10X-RAY DIFFRACTION10B373 - 451
11X-RAY DIFFRACTION11B452 - 500
12X-RAY DIFFRACTION12B501 - 529

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