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- PDB-4nq8: Crystal structure of a trap periplasmic solute binding protein fr... -

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Entry
Database: PDB / ID: 4nq8
TitleCrystal structure of a trap periplasmic solute binding protein from Bordetella bronchispeptica (bb3421), target EFI-510039, with density modeled as pantoate
ComponentsPutative periplasmic substrate-binding transport protein
KeywordsPROTEIN TRANSPORT / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PANTOATE / Putative periplasmic substrate-binding transport protein / Putative periplasmic substrate-binding transport protein
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionNov 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative periplasmic substrate-binding transport protein
B: Putative periplasmic substrate-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6218
Polymers74,0642
Non-polymers5576
Water12,809711
1
A: Putative periplasmic substrate-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4075
Polymers37,0321
Non-polymers3754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative periplasmic substrate-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2153
Polymers37,0321
Non-polymers1832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-35 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.004, 56.352, 75.609
Angle α, β, γ (deg.)99.210, 92.010, 106.230
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative periplasmic substrate-binding transport protein


Mass: 37031.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB50 / Gene: BB3421 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WGZ0, UniProt: A0A0H3LPK2*PLUS
#2: Chemical ChemComp-PAF / PANTOATE / 2,4-DIHYDROXY-3,3-DIMETHYL-BUTYRATE / Pantoic acid


Mass: 147.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (36.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (MCSG1(F10), 2.0 M Ammonium Sulfate 0.1 M Tris); Cryoprotection (20% reservoir, 80% of 2.0 M Lithium Sulfate, Ligand Copurified ...Details: Protein (36.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (MCSG1(F10), 2.0 M Ammonium Sulfate 0.1 M Tris); Cryoprotection (20% reservoir, 80% of 2.0 M Lithium Sulfate, Ligand Copurified with Protein), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 8, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→74.37 Å / Num. all: 88845 / Num. obs: 88845 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 15.88 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.583.60.6721.145517127030.67289.5
1.58-1.683.60.4711.643716122040.47190.2
1.68-1.793.60.3112.541108114760.31190.8
1.79-1.943.60.1953.838537107370.19591.2
1.94-2.123.60.1146.43557899080.11491.5
2.12-2.373.60.0917.33213889940.09192.1
2.37-2.743.60.06210.72897680370.06292.9
2.74-3.353.60.04812.32456068250.04893.5
3.35-4.743.60.03517.11897152660.03593.5
4.74-25.2963.50.03316.7942026950.03387.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Same crystal form solved by Iodine SAD phasing.

Resolution: 1.5→25.296 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8815 / SU ML: 0.17 / σ(F): 0 / σ(I): 0 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.184 4383 4.93 %RANDOM
Rwork0.1579 ---
obs0.1593 88820 91.22 %-
all-88820 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.17 Å2 / Biso mean: 21.9339 Å2 / Biso min: 7.67 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4550 0 32 711 5293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014667
X-RAY DIFFRACTIONf_angle_d1.2636327
X-RAY DIFFRACTIONf_chiral_restr0.07716
X-RAY DIFFRACTIONf_plane_restr0.007821
X-RAY DIFFRACTIONf_dihedral_angle_d13.8091723
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 (%)
1.5-1.5170.28341350.26492717285289
1.517-1.53490.29931360.27222773290990
1.5349-1.55360.31131410.26542843298490
1.5536-1.57330.29041430.24522741288489
1.5733-1.5940.28221370.23872755289290
1.594-1.61580.26551550.23192826298190
1.6158-1.63890.24031440.20932772291690
1.6389-1.66330.27421540.2082739289390
1.6633-1.68930.20531500.192807295791
1.6893-1.7170.20451510.18252792294391
1.717-1.74660.2321320.17862811294391
1.7466-1.77840.21141470.16652798294591
1.7784-1.81260.18471520.16042805295791
1.8126-1.84950.15521320.15672807293991
1.8495-1.88980.23961630.18532798296191
1.8898-1.93370.27281480.21742837298592
1.9337-1.9820.17391490.15832775292491
1.982-2.03560.16281420.13232861300392
2.0356-2.09550.1641320.12892830296291
2.0955-2.16310.16191200.13162914303492
2.1631-2.24030.20291420.16442769291192
2.2403-2.330.17991390.1762849298892
2.33-2.43590.17271670.13762860302793
2.4359-2.56430.191470.13752881302893
2.5643-2.72470.17511410.14552859300093
2.7247-2.93480.17441430.15222891303494
2.9348-3.22960.19481410.14732908304993
3.2296-3.69570.16211620.13822846300894
3.6957-4.65150.11721650.12122873303893
4.6515-25.29990.17811730.15782700287388
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)
10.5135-0.51240.08561.8421-0.10390.48560.02330.0505-0.011-0.1759-0.026-0.2520.05230.12660.00280.15850.01950.02560.1294-0.0120.16984.666629.926512.5872
20.57920.2238-0.21470.9923-0.31941.351-0.03990.0403-0.0238-0.10870.04550.12590.0741-0.16230.00080.1256-0.001-0.00530.1313-0.00460.1351-9.88133.282214.0023
30.5295-0.03270.13711.2634-0.12850.7332-0.0011-0.06750.01070.13640.02690.0942-0.0465-0.1007-0.02150.10180.01150.01760.11650.00210.1054-9.019645.122126.106
40.3915-0.48850.05931.93980.25330.620.02620.0007-0.07040.04490.0008-0.16290.06890.0684-0.020.09460.00610.00120.0949-0.00070.12292.281132.554622.5867
50.73310.0915-0.34160.879-0.22041.02130.059-0.10660.06140.2298-0.02090.1012-0.0979-0.099-0.03030.1990.01090.00540.1784-0.00740.1357-11.617149.396635.4236
65.0049-0.75760.1842.30120.14072.93710.0238-0.64240.02390.50960.00310.07340.16510.2138-0.05010.292-0.02080.02920.26340.07110.1754-11.773332.413541.838
70.8790.623-0.20221.16110.1370.75050.03590.0384-0.04960.0890.0193-0.3292-0.08780.1719-0.02680.1451-0.0158-0.02820.16780.0040.20111.124855.95423.7368
80.34560.101-0.19051.2284-0.011.3052-0.01570.02860.10370.13620.05130.0545-0.2286-0.1964-0.02920.15430.02710.00930.1363-0.00020.1361-3.709759.22312.0335
90.81410.25670.23240.7508-0.2321.201-0.01830.17060.0465-0.07910.04060.0188-0.0723-0.0811-0.00830.13340.00090.01090.18210.01010.101-4.231353.9155-14.2567
100.94310.37440.39230.8959-0.28710.75880.01260.150.1204-0.07570.07970.19910.0081-0.4517-0.05210.1056-0.0090.00450.32030.03140.1777-17.437848.0686-9.5388
110.72470.2066-0.03070.5292-0.19921.2218-0.01020.01910.04770.0340.01140.05330.036-0.1101-0.00390.10780.0002-0.0050.1251-0.00480.1089-4.866946.8103-3.6482
121.13881.49280.16843.34970.3851.3233-0.02510.1081-0.10450.03960.0594-0.2727-0.02850.2308-0.0550.12810.0026-0.00720.1813-0.00530.1758.624149.329-8.3328
130.61260.1090.29511.3413-0.81311.5797-0.04850.0564-0.0104-0.17650.18830.17030.2405-0.3702-0.15310.1937-0.0293-0.02210.26310.03040.1332-13.236546.7686-20.2733
143.60530.03330.29382.52850.1582.94990.20840.49740.07-0.41990.00120.116-0.2340.0793-0.19820.26360.0182-0.00420.32180.09160.1779-5.686861.3324-25.8603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 64 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 98 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 231 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 232 through 284 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 285 through 311 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 312 through 325 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 64 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 65 through 98 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 99 through 163 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 164 through 191 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 192 through 249 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 250 through 285 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 286 through 311 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 312 through 325 )B0

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