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- PDB-4n8y: Crystal structure of a trap periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4n8y
TitleCrystal structure of a trap periplasmic solute binding protein from bradyrhizobium sp. btai1 b (bbta_0128), target EFI-510056 (bbta_0128), complex with alpha/beta-d-galacturonate
ComponentsPutative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
KeywordsTRANSPORT PROTEIN / 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
alpha-D-galactopyranuronic acid / beta-D-galactopyranuronic acid / Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
DepositionOct 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
B: Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8196
Polymers72,0432
Non-polymers7774
Water16,358908
1
A: Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4103
Polymers36,0211
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4103
Polymers36,0211
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.798, 85.705, 86.246
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 Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)


Mass: 36021.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Strain: BTAi1 / Gene: BBta_0128 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5E8D2
#2: Sugar ChemComp-ADA / alpha-D-galactopyranuronic acid / alpha-D-galacturonic acid / D-galacturonic acid / galacturonic acid / ALPHA D-GALACTURONIC ACID / D-Galacturonic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid / D-Galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (56.1 mg/ml, 10 mM HEPES, 5 mM DTT, 10 mM D-Galacturonate); Reservoir (0.1 M HEPES, 25 %(w/v) PEG 3350); Cryoprotection (20% Reservoir, 80% PEG3350 (50% w/v)), pH 7.5, VAPOR ...Details: Protein (56.1 mg/ml, 10 mM HEPES, 5 mM DTT, 10 mM D-Galacturonate); Reservoir (0.1 M HEPES, 25 %(w/v) PEG 3350); Cryoprotection (20% Reservoir, 80% PEG3350 (50% w/v)), pH 7.5, 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: 0.971 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 9, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 1.5→86.246 Å / Num. all: 90134 / Num. obs: 90134 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 22.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.587.30.5231.593789127930.52394.4
1.58-1.687.50.3632.291527121840.36395
1.68-1.797.60.2483.188116115690.24895.5
1.79-1.947.60.1574.982347107680.15796.1
1.94-2.127.60.0977.776238100330.09796.5
2.12-2.377.60.06611.26923091440.06697
2.37-2.747.50.04715.36140181410.04797.5
2.74-3.357.50.03121.65208769540.03198
3.35-4.747.30.02228.14022254840.02298.3
4.74-85.7056.90.0229.92117330640.0295.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4N17

4n17


Resolution: 1.5→29.087 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9015 / SU ML: 0.13 / σ(F): 0 / σ(I): 0 / Phase error: 16.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1751 4506 5.01 %RANDOM
Rwork0.1436 ---
obs0.1452 90027 95.8 %-
all-90027 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.83 Å2 / Biso mean: 22.6948 Å2 / Biso min: 6.48 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 52 908 5592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094809
X-RAY DIFFRACTIONf_angle_d1.2156521
X-RAY DIFFRACTIONf_chiral_restr0.05738
X-RAY DIFFRACTIONf_plane_restr0.007840
X-RAY DIFFRACTIONf_dihedral_angle_d13.3751813
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 (%)
1.5-1.51710.26891370.21972796293394
1.5171-1.53490.23251660.20162723288994
1.5349-1.55360.21081410.20072779292094
1.5536-1.57330.23171500.18432773292394
1.5733-1.5940.22241570.17992763292094
1.594-1.61580.18451450.17492776292195
1.6158-1.63890.1861400.17982807294795
1.6389-1.66340.21661390.16962782292194
1.6634-1.68930.21161390.16592805294495
1.6893-1.7170.19221400.16842825296595
1.717-1.74660.20021450.16352818296395
1.7466-1.77840.19371510.15822774292595
1.7784-1.81260.20811510.15592838298996
1.8126-1.84960.18761570.14852800295796
1.8496-1.88980.18611560.1512823297996
1.8898-1.93380.18521490.15112855300496
1.9338-1.98210.17971350.15262855299096
1.9821-2.03570.19771410.14912852299396
2.0357-2.09560.18771580.15032865302396
2.0956-2.16320.16531420.1432881302396
2.1632-2.24050.17211500.14132865301597
2.2405-2.33010.18051670.13362877304497
2.3301-2.43610.15421380.13452897303597
2.4361-2.56450.16241490.12972892304197
2.5645-2.72510.15171720.13392909308197
2.7251-2.93530.16051600.1342909306997
2.9353-3.23030.1621510.13322956310798
3.2303-3.6970.15831520.13252987313998
3.697-4.65470.16821600.11572996315698
4.6547-29.09240.15741680.14543043321195
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)
10.93660.6204-0.82851.0165-0.62451.02730.0277-0.01330.0561-0.0337-0.0929-0.1341-0.05890.090.07290.1098-0.00120.01560.12050.00730.114723.05625.674-15.8358
20.50040.15980.10941.1684-0.01580.36980.0280.0468-0.0299-0.2259-0.04830.18660.0234-0.07870.01550.15370.0151-0.02480.1367-0.02770.13317.69218.1237-18.0287
30.6834-0.13480.11891.5880.07220.6461-0.0069-0.0028-0.1426-0.0887-0.01950.30140.0371-0.09610.02050.0854-0.00040.01210.1032-0.02510.16567.47147.9117-12.1126
40.45930.04940.01851.3941-0.37860.585-0.02410.0508-0.0398-0.2019-0.0628-0.07550.01160.05650.07260.13010.00690.02960.109-0.01210.090318.446814.4917-18.1674
51.2884-0.0180.74141.08040.21551.31950.08470.2431-0.3455-0.152-0.00530.36780.1742-0.0232-0.0920.1572-0.0156-0.02840.1947-0.06460.28223.7707-3.5235-16.4148
65.4906-0.8032-0.01081.2715-0.06991.6177-0.08560.14370.1242-0.38950.01150.25170.0767-0.00510.04540.4272-0.0237-0.13690.2528-0.06760.25283.87596.9591-33.7659
70.901-0.72210.98421.1133-0.60091.14130.0042-0.0184-0.0751-0.0131-0.1106-0.22580.14850.14950.10370.11940.03470.03750.15120.06020.168722.175517.396413.3136
80.4161-0.2664-0.27351.25180.23320.7431-0.05-0.0502-0.06190.0186-0.03550.05170.0691-0.00760.08310.08030.00610.01810.11960.02170.09736.631124.842914.8243
90.57150.0752-0.17650.9301-0.07490.7839-0.0285-0.0372-0.0191-0.0192-0.06030.0725-0.0389-0.01970.08510.07290.0154-0.0070.0973-0.00210.08937.444833.31710.0897
100.2788-0.15760.15431.8655-1.35181.8532-0.0421-0.1015-0.04610.1675-0.141-0.2044-0.0990.2380.17960.08890.0035-0.01170.16070.05260.143822.256229.190416.2119
110.5733-0.0102-0.00331.08310.02690.44350.0796-0.11150.10430.0556-0.10620.1737-0.1726-0.0096-0.00020.14890.0027-0.00530.1456-0.02480.14852.271347.072312.4523
125.20461.30521.12332.31180.00331.84630.1789-0.45290.11310.3297-0.08180.20590.1254-0.0652-0.06280.2497-0.00210.04910.27970.00820.15221.670136.541830.1297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 61 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 109 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 219 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 220 through 281 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 307 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 308 through 322 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 61 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 109 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 246 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 247 through 281 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 282 through 306 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 307 through 322 )B0

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