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

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Basic information

Entry
Database: PDB / ID: 4pfb
TitleCrystal structure of a TRAP periplasmic solute binding protein from Fusobacterium nucleatun (FN1258, TARGET EFI-510120) with bound SN-glycerol-3-phosphate
ComponentsC4-dicarboxylate-binding protein
KeywordsTRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transmembrane transport / metal ion binding
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SN-GLYCEROL-3-PHOSPHATE / IMIDAZOLE / C4-dicarboxylate-binding protein
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C4-dicarboxylate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2909
Polymers39,6531
Non-polymers6378
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-109 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.574, 113.574, 79.937
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

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Components

#1: Protein C4-dicarboxylate-binding protein


Mass: 39652.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (bacteria)
Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: FN1258 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RE65
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (70.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM Glycerol 3-phosphate); Reservoir (0.2 M Zinc Acetate, 0.1 M Imidazole pH 6.5, 10 %(w/v) PEG 8000); Cryoprotection (80% Reservoir + 20% Glycerol

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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: Dec 6, 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: 2.7→113.574 Å / Num. all: 14902 / Num. obs: 14902 / % possible obs: 99.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 52.93 Å2 / Rpim(I) all: 0.05 / Rrim(I) all: 0.173 / Rsym value: 0.166 / Net I/av σ(I): 3.666 / Net I/σ(I): 10.4 / Num. measured all: 175821
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.7-2.85120.8540.92568221350.2540.8543.1100
2.85-3.02120.5421.42427520160.1620.5424.6100
3.02-3.23120.3572.12285319030.1070.3576.5100
3.23-3.49120.2353.22134317830.070.2359.3100
3.49-3.8211.90.164.41952416370.0480.1612.4100
3.82-4.2711.90.1384.61780514990.0420.13814.9100
4.27-4.9311.70.1441575713420.0420.1416.5100
4.93-6.0411.60.1354.41330211500.0410.13516.5100
6.04-8.5411.20.0877102339110.0270.08718.2100
8.54-46.2959.60.05910.750475260.020.05918.296.4

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N6K

4n6k


Resolution: 2.7→40.154 Å / FOM work R set: 0.871 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 753 5.06 %Random Selection
Rwork0.1644 14117 --
obs0.1663 14870 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.09 Å2 / Biso mean: 40.85 Å2 / Biso min: 16.05 Å2
Refinement stepCycle: final / Resolution: 2.7→40.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 25 81 2525
Biso mean--44.99 35.24 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122496
X-RAY DIFFRACTIONf_angle_d1.0943378
X-RAY DIFFRACTIONf_chiral_restr0.072380
X-RAY DIFFRACTIONf_plane_restr0.006436
X-RAY DIFFRACTIONf_dihedral_angle_d15.4914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.90840.28441830.21727292912100
2.9084-3.2010.24581420.195127822924100
3.201-3.66390.21741590.166127872946100
3.6639-4.61510.18321300.136328422972100
4.6151-40.15890.1721390.16392977311699
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)
10.82220.04020.93113.35250.91061.23730.1443-0.364-0.32680.002-0.2034-0.13830.1249-0.0510.07610.2670.01430.04960.18880.10890.275910.105753.681247.6407
22.8436-0.03131.18672.5030.95213.05080.0965-0.2001-0.2779-0.2958-0.138-0.22270.25880.07870.03650.30710.16340.05620.23070.0270.231214.493448.534347.6815
30.82180.05530.4442.72260.2623.85620.02920.0124-0.375-0.1917-0.2938-0.8192-0.04711.34990.06660.34740.05190.18770.48680.0730.472624.78256.708142.18
41.47580.1855-0.46971.6858-0.61020.8422-0.04410.09620.2221-0.1827-0.0282-0.3979-0.49960.57430.02940.3652-0.180.01010.36450.08820.346521.397671.952447.2111
51.1328-0.05380.32683.13851.10732.0511-0.01330.17720.1267-0.0735-0.1022-0.5878-0.0490.27810.10360.3493-0.06510.04980.31910.08950.287117.542564.68744.4522
60.9945-0.4421-0.32045.09513.85464.8238-0.07850.20950.1304-0.2067-0.37090.5398-0.3996-0.18010.34420.36730.0098-0.00490.18440.07440.3115.390963.636945.1045
71.83060.0569-1.59110.2234-0.35282.1940.03430.33850.33780.0475-0.1233-0.245-0.43070.244-0.0080.685-0.28490.02870.5850.1280.524724.118781.799644.341
82.531-0.1571-0.48181.2182-0.10820.6534-0.07790.46070.4552-0.5977-0.14250.0077-0.40490.1912-0.22110.9803-0.3378-0.00240.21530.52210.290915.636480.66428.7037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 53 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 70 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 95 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 220 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 248 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 283 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 284 through 313 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 314 through 330 )A0

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