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- PDB-4pfi: Crystal structure of a tRAP periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4pfi
TitleCrystal structure of a tRAP periplasmic solute binding protein from marinobacter aquaeolei VT8 (Maqu_2829, TARGET EFI-510133), apo open structure
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
Similarity search - Function
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRAP dicarboxylate transporter-DctP subunit
Similarity search - Component
Biological speciesMarinobacter aquaeolei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3024 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
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
DepositionApr 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Data collection
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_symmetry / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)38,7302
Polymers38,7071
Non-polymers231
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.841, 85.841, 170.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

21A-532-

HOH

31A-536-

HOH

41A-618-

HOH

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Components

#1: Protein TRAP dicarboxylate transporter-DctP subunit


Mass: 38706.977 Da / Num. of mol.: 1 / Fragment: TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter aquaeolei (bacteria) / Strain: ATCC 700491 / DSM 11845 / VT8 / Gene: Maqu_2829 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1U4I5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (55.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (3.5 M Sodium Format pH 7.0); Cryoprotection (80% 7M Sodium Formate + 20% Reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 24, 2014 / 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: 2.3→100 Å / Num. obs: 17145 / % possible obs: 99.7 % / Redundancy: 41.5 % / Rmerge(I) obs: 0.146 / Χ2: 1.058 / Net I/av σ(I): 29.183 / Net I/σ(I): 7.1 / Num. measured all: 711896
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.3-2.3441.28360.838100
2.34-2.3842.58480.834100
2.38-2.4342.58150.83100
2.43-2.4842.58380.876100
2.48-2.5342.68380.867100
2.53-2.5942.68390.8991000.807
2.59-2.6642.28380.9231000.719
2.66-2.7342.78290.9231000.619
2.73-2.8142.58520.9341000.48
2.81-2.942.38410.9861000.37
2.9-342.48371.0251000.306
3-3.1242.38531.0751000.235
3.12-3.2642.28541.121000.183
3.26-3.44428621.2211000.151
3.44-3.6541.88531.3071000.136
3.65-3.9341.48731.4951000.127
3.93-4.3340.88731.7061000.127
4.33-4.9640.88851.4921000.109
4.96-6.2440.19120.9581000.079
6.24-10034.59690.80395.70.073

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3024→28.336 Å / FOM work R set: 0.834 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1568 5.09 %Random Selection
Rwork0.1856 29260 --
obs0.1879 30828 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.64 Å2 / Biso mean: 31.63 Å2 / Biso min: 2.03 Å2
Refinement stepCycle: final / Resolution: 2.3024→28.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 1 144 2519
Biso mean--6.71 33.22 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112431
X-RAY DIFFRACTIONf_angle_d1.1393305
X-RAY DIFFRACTIONf_chiral_restr0.07362
X-RAY DIFFRACTIONf_plane_restr0.005441
X-RAY DIFFRACTIONf_dihedral_angle_d15.211875
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 (%)
2.3024-2.37670.32391350.2432605274096
2.3767-2.46160.25231390.24172672281199
2.4616-2.56010.2911440.224226532797100
2.5601-2.67660.32031500.214926872837100
2.6766-2.81760.28441590.218126282787100
2.8176-2.99390.26131480.194326612809100
2.9939-3.22480.2431370.17727062843100
3.2248-3.54870.20461550.159426542809100
3.5487-4.0610.18731530.15562644279799
4.061-5.11150.16961290.148826782807100
5.1115-28.3380.2371190.20112672279199
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)
11.87340.6964-0.80111.415-0.160.72640.1859-0.3412-0.3090.1058-0.1298-0.07210.4015-0.07850.00810.4059-0.1019-0.10390.24860.1130.282534.008841.1337.7014
21.3173-0.63040.18512.0280.81341.71050.0537-0.0767-0.2131-0.00560.0388-0.12680.24640.1764-0.0620.17260.0284-0.01030.10620.02950.120344.037361.36561.4754
31.32980.29540.08091.1765-0.16830.79950.1653-0.0338-0.5679-0.2138-0.05310.01360.49230.07190.07280.4030.0128-0.08020.10850.03050.326438.629745.0317-0.8801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 165 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 254 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 349 )A0

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