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- PDB-4n15: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Entry
Database: PDB / ID: 4n15
TitleCrystal structure of a TRAP periplasmic solute binding protein from Burkholderia ambifaria (BAM_6123), Target EFI-510059, with bound beta-D-glucuronate
ComponentsTRAP dicarboxylate transporter, 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 / carbohydrate binding
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
beta-D-glucopyranuronic acid / Solute-binding protein Bamb_6123
Similarity search - Component
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Zhao, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Zhao, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / 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 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 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

Downloads & links

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1253
Polymers36,9061
Non-polymers2182
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.190, 101.781, 55.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-749-

HOH

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit / TRAP periplasmic solute binding protein


Mass: 36906.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: ATCC BAA-244 / AMMD / Gene: Bamb_6123 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B2F6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 1.84 Å3/Da / Density % sol: 33.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 59.1 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-glucuronic acid, reservoir: 0.2 M magnesium acetate, 20% w/v PEG3350 (MCSG1 C5), cryoprotection: 4:1 50% w/v PEG3350:reservoir, ...Details: 59.1 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-glucuronic acid, reservoir: 0.2 M magnesium acetate, 20% w/v PEG3350 (MCSG1 C5), cryoprotection: 4:1 50% w/v PEG3350:reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 21, 2013 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→100 Å / Num. all: 32282 / Num. obs: 32282 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 14.59 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Χ2: 0.924 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.683.10.36514730.684190
1.68-1.713.90.33416060.786198.3
1.71-1.744.40.29316190.8011100
1.74-1.784.40.26216430.871199.9
1.78-1.824.50.24116280.8781100
1.82-1.864.30.20616401.01199.9
1.86-1.94.40.18616301.027199.9
1.9-1.964.50.16116291.0691100
1.96-2.014.60.13816341.0421100
2.01-2.084.60.12516291.0831100
2.08-2.154.60.11316421.099199.7
2.15-2.244.70.10616311.218199
2.24-2.344.70.09816291.268198.6
2.34-2.464.80.0916221.192197.9
2.46-2.624.90.08515961.174197.2
2.62-2.824.90.07716221.109197
2.82-3.114.90.06615980.903196.6
3.11-3.554.90.05116100.608195.8
3.55-4.484.90.03816000.376194.5
4.48-1004.90.02816010.191189.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
HKL-3000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LN5

4ln5


Resolution: 1.651→22.067 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8784 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 19.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 1572 5.05 %RANDOM
Rwork0.1583 ---
all0.1603 31126 --
obs0.1603 31126 94.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.71 Å2 / Biso mean: 22.7023 Å2 / Biso min: 6.02 Å2
Refinement stepCycle: LAST / Resolution: 1.651→22.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 14 302 2643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112397
X-RAY DIFFRACTIONf_angle_d1.2733250
X-RAY DIFFRACTIONf_chiral_restr0.074358
X-RAY DIFFRACTIONf_plane_restr0.007422
X-RAY DIFFRACTIONf_dihedral_angle_d13.004895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.651-1.70450.28551000.19892069216973
1.7045-1.76540.28151250.19242470259588
1.7654-1.83610.21621430.19022687283095
1.8361-1.91960.20411680.19062752292098
1.9196-2.02070.2171450.180428092954100
2.0207-2.14720.22581350.166728472982100
2.1472-2.31290.19671590.15522817297699
2.3129-2.54530.21961480.1542787293598
2.5453-2.91290.2341350.15832796293197
2.9129-3.66720.14951660.1492745291196
3.6672-22.06860.15971480.13242775292392
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)
11.46920.25360.18060.7491-0.02350.9385-0.05940.09930.1937-0.04620.014-0.0995-0.2320.18810.03520.0969-0.0251-0.01230.13460.03770.134335.426526.51191.425
21.82120.0344-0.76440.9111-0.13821.3247-0.04080.2345-0.0702-0.02640.0332-0.07450.25320.1303-0.00810.10780.0129-0.00480.1306-0.0110.096234.802612.9043-0.4799
31.08190.2662-0.18631.11250.20170.41980.1667-0.1447-0.01480.1498-0.0948-0.0190.33510.0242-0.00870.2618-0.0009-0.03520.06950.00390.091629.99429.57217.8865
40.57230.104-0.04010.54180.10920.59120.0355-0.0382-0.02750.2084-0.0422-0.00720.18070.05310.00470.1260.0076-0.00430.0837-0.00190.090433.442712.458311.7415
50.8018-0.0025-0.04040.6101-0.08570.61320.0152-0.0569-0.08410.5236-0.18830.45950.2914-0.17440.25560.172-0.17610.2260.1053-0.03030.205813.91123.33737.7627
60.72410.24570.25340.7432-0.0530.6911-0.18170.26590.0105-0.08190.07480.1950.0909-0.33380.05930.0808-0.07050.0080.1929-0.03130.122613.92614.74612.0402
71.76240.0523-0.17490.66310.34940.6909-0.09490.23150.00530.1113-0.00470.05020.1525-0.03530.03150.098-0.01330.00940.1217-0.00840.076726.957415.70987.074
82.50960.0613-0.12030.48370.14270.7258-0.0137-0.02150.15970.0621-0.02150.0583-0.0530.02610.01590.07750.0028-0.01510.0841-0.01030.11230.123325.763912.5311
90.7907-0.55060.03561.3340.24430.1359-0.1862-0.1328-0.05930.7452-0.02450.26260.4647-0.1444-0.11940.5414-0.03320.0880.1849-0.0080.169615.18964.953618.5801
102.348-1.083-0.89623.88731.84093.5010.24890.1244-0.124-0.2899-0.1675-0.0239-0.02310.1512-0.03310.3-0.0303-0.07860.15740.05440.163235.67491.589121.4692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 72 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 95 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 123 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 153 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 191 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 216 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 217 through 249 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 250 through 284 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 311 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 312 through 327 )A0

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