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- PDB-5owf: Structure of a LAO-binding protein mutant with glutamine -

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Basic information

Entry
Database: PDB / ID: 5owf
TitleStructure of a LAO-binding protein mutant with glutamine
ComponentsLysine/arginine/ornithine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / ligand specificity / protein design / binding pocket / periplasmatic binding protein
Function / homology
Function and homology information


amino acid transport / outer membrane-bounded periplasmic space
Similarity search - Function
Specific amino acids and opine-binding periplasmic protein, ABC transporter / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / DI(HYDROXYETHYL)ETHER / Lysine/arginine/ornithine-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsShanmugaratnam, S. / Banda-Vazquez, J. / Sosa-Peinado, A. / Hocker, B.
Funding support Germany, Mexico, 3items
OrganizationGrant numberCountry
German Research FoundationHO 4022/2-3 Germany
CONACyT167838 Mexico
PapiitIN214512-3 Mexico
CitationJournal: Protein Sci. / Year: 2018
Title: Redesign of LAOBP to bind novel l-amino acid ligands.
Authors: Banda-Vazquez, J. / Shanmugaratnam, S. / Rodriguez-Sotres, R. / Torres-Larios, A. / Hocker, B. / Sosa-Peinado, A.
History
DepositionAug 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_name_com / entity_src_gen / pdbx_entity_nonpoly / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_nonpoly.name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Apr 25, 2018Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine/arginine/ornithine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,93123
Polymers28,3771
Non-polymers1,55422
Water2,612145
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint50 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.972, 58.730, 115.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine/arginine/ornithine-binding periplasmic protein / LAO-binding protein


Mass: 28376.895 Da / Num. of mol.: 1 / Mutation: L138K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: argT, STM2355 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02911

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Non-polymers , 5 types, 167 molecules

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


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 145 / 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: 2.43 Å3/Da / Density % sol: 49.32 % / Description: cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 150 mM potassium bromide, 30 % (wt/vol) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 1, 2017
RadiationMonochromator: Si111 DCM with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.91→41.14 Å / Num. obs: 20131 / % possible obs: 99.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 29.0530958083 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1741 / Rpim(I) all: 0.05782 / Net I/σ(I): 8.7
Reflection shellResolution: 1.91→2.03 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.954 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 1946 / CC1/2: 0.375 / Rpim(I) all: 0.7327 / % possible all: 97.49

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Processing

Software
NameVersionClassification
XDSBUILT=20170615data reduction
PHENIX1.12_2829refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LAF

1laf


Resolution: 1.91→41.14 Å / SU ML: 0.201763309589 / Cross valid method: FREE R-VALUE / σ(F): 1.35048228562 / Phase error: 23.6496531516
RfactorNum. reflection% reflection
Rfree0.231402868687 1007 5.0022353584 %
Rwork0.18955398062 --
obs0.191660731496 20131 99.5253868591 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.6270379095 Å2
Refinement stepCycle: LAST / Resolution: 1.91→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 101 145 2061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006336184986291941
X-RAY DIFFRACTIONf_angle_d0.7603071590092575
X-RAY DIFFRACTIONf_chiral_restr0.049882353218275
X-RAY DIFFRACTIONf_plane_restr0.00413479667666330
X-RAY DIFFRACTIONf_dihedral_angle_d3.629682106071590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9099-2.01060.3168183079771390.2989419354972641X-RAY DIFFRACTION98.0253878702
2.0106-2.13650.3005791324751410.2412840106332683X-RAY DIFFRACTION99.8232591022
2.1365-2.30150.2624246143611430.2053502691262712X-RAY DIFFRACTION99.8251748252
2.3015-2.5330.2388274951761420.1893715434742699X-RAY DIFFRACTION99.8594024605
2.533-2.89950.2233614412081440.1802481870242730X-RAY DIFFRACTION99.7916666667
2.8995-3.65270.2118564356471450.1680245144512767X-RAY DIFFRACTION99.6918863403
3.6527-41.15290.2146250960191530.1793890443112892X-RAY DIFFRACTION99.6726677578
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)
15.28256792133-0.5014269521940.6611241893914.298167732030.5535281616165.020161444740.166070158878-0.03939179167760.2073817810890.0836606212143-0.0181934764673-0.206010562256-0.3061550846890.158521239862-0.1757702994150.151998853403-0.0207707922031-0.002263326480660.219917805216-0.007540772254530.16412131066428.629814484865.170862072947.0385127668
27.1423313961-5.10725484785-0.2164964421417.24220408124-0.2039755158711.90382809041-0.2035696268790.07158339405730.3655589792770.1224405944930.27611791284-0.342694226142-0.5233693859850.0840245330137-0.04188701059670.29935585651-0.08170657315760.01657364880720.298835982120.003718282949880.23060417147530.304756904869.924434807240.9072797798
33.121342192840.09190068576940.8237229046213.44145390890.2529104098343.23281025607-0.0229586722766-0.09812541176440.2201749846160.155358686242-0.0361128513786-0.0865296817772-0.1937078322760.1322665950910.04494855833540.1618741988850.01668080977830.0303968084740.2318902057840.002778623149120.1632984357119.664496017566.770778650750.1037875649
43.12385717320.490906818081-0.8655299928453.390990338420.1610140803573.75434573245-0.09737937882220.152990708696-0.448845072933-0.05415013230580.0806582179198-0.3434379076650.419848072438-0.1616815367060.01836095024950.222801514011-0.01578594919820.000604403331430.184539825259-0.02090053371560.21309045814821.89010149844.111545204346.2277561471
51.56002981073-0.016542286713-0.621885409373.74243141329-0.7000192533021.58889020445-0.01197882412940.220208762340.203556681079-0.3294186009850.1231422676860.0769018145152-0.134680758109-0.148550261318-0.08575855480860.2330728625020.0144490204251-0.05514921864980.3393882840860.02023258272710.20933872451917.410362774266.335722754638.5985023786
61.999904476251.894975548393.648398774796.34227962312-1.342395120851.594743453390.83144644869-2.4804494857-0.2557103162080.6036521163780.421627092915-3.33128810272-0.1783941031398.73597710259-1.214221405280.3906580225850.04750521718090.03677548224910.904385948331-0.1097370103280.6116868353219.809376090757.241721291147.3692636984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 201 )
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 259 )
6X-RAY DIFFRACTION6chain 'E' and (resid 1 through 1 )

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