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- PDB-4p9k: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4p9k
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER EISENIAE EF01-2 (Veis_3954, TARGET EFI-510324) A NEPHRIDIAL SYMBIONT OF THE EARTHWORM EISENIA FOETIDA, BOUND TO D-ERYTHRONATE WITH RESIDUAL DENSITY SUGGESTIVE OF SUPERPOSITION WITH COPURIFIED ALTERNATIVE LIGAND.
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
(2R,3R)-2,3,4-trihydroxybutanoic acid / Solute-binding protein Veis_3954
Similarity search - Component
Biological speciesVerminephrobacter eiseniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 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 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Aug 26, 2015Group: Data collection
Revision 1.4Sep 20, 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 / _software.name
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 16, 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)36,3972
Polymers36,2611
Non-polymers1361
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.290, 76.290, 110.813
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-646-

HOH

21A-659-

HOH

Detailsbiological unit is a monomer

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 36260.734 Da / Num. of mol.: 1 / Fragment: TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verminephrobacter eiseniae (bacteria) / Strain: EF01-2 / Gene: Veis_3954 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1WPV4
#2: Chemical ChemComp-EAX / (2R,3R)-2,3,4-trihydroxybutanoic acid / erythronic acid


Mass: 136.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (42.92 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Erythronate); Reservoir ( 0.1 M Tris pH 8.5 2.4 M di-Ammonium Phosphate ); Cryoprotection (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: Mar 21, 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: 1.4→110.81 Å / Num. obs: 142034 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 14.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.032 / Net I/σ(I): 16 / Num. measured all: 1228244 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.4-1.4216.42.2871.75916836130.7290.579100
7.67-110.8113.50.0746.171635310.9980.01999.2

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Processing

Software
NameVersionClassification
MOSFLM0.1.27data reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→26.535 Å / FOM work R set: 0.8896 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.168 7193 5.06 %Random Selection
Rwork0.1479 134841 --
obs0.1489 142034 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.39 Å2 / Biso mean: 19.69 Å2 / Biso min: 6.89 Å2
Refinement stepCycle: final / Resolution: 1.4→26.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 9 475 2810
Biso mean--10.02 31.77 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122437
X-RAY DIFFRACTIONf_angle_d1.2023303
X-RAY DIFFRACTIONf_chiral_restr0.073368
X-RAY DIFFRACTIONf_plane_restr0.006443
X-RAY DIFFRACTIONf_dihedral_angle_d13.354909
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.41590.33272000.310845524752
1.4159-1.43260.32192180.289145284746
1.4326-1.450.29632260.288644674693
1.45-1.46840.28822300.26845414771
1.4684-1.48770.28282260.251344084634
1.4877-1.50810.26642800.236544974777
1.5081-1.52960.22932140.227945634777
1.5296-1.55250.2282600.215844644724
1.5525-1.57670.2252500.210244824732
1.5767-1.60260.20552060.189145254731
1.6026-1.63020.20772400.182244814721
1.6302-1.65980.1992530.178644774730
1.6598-1.69180.18612120.164245294741
1.6918-1.72630.16862660.162544614727
1.7263-1.76380.16242470.153444714718
1.7638-1.80480.17362590.146144804739
1.8048-1.850.1732320.143645204752
1.85-1.90.15612520.138744904742
1.9-1.95590.16412380.139245204758
1.9559-2.0190.17412550.133744714726
2.019-2.09110.14312410.125844774718
2.0911-2.17480.15352600.122244844744
2.1748-2.27370.15572680.124544634731
2.2737-2.39350.15092160.117545174733
2.3935-2.54340.16082120.124945374749
2.5434-2.73960.14922410.129745134754
2.7396-3.01490.15192450.136644434688
3.0149-3.45040.16192600.140745184778
3.4504-4.3440.12952610.117944514712
4.344-26.54020.1622250.143245114736
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)
11.49150.76090.07790.98760.01710.1551-0.01350.16210.16740.04520.10780.23650.1401-0.4274-0.10730.1358-0.0340.01530.24180.05720.1306-12.436844.200139.6326
22.21430.1195-1.54870.8114-0.11011.4041-0.13070.0801-0.12820.03570.18250.24990.2949-0.4192-0.01990.162-0.07660.01220.23650.06530.1783-13.712438.800943.4808
30.85580.0015-0.2150.3816-0.18660.9828-0.0028-0.07640.1130.10640.0433-0.0021-0.0622-0.0829-0.0420.14860.01670.0150.0829-0.00130.10980.362449.629150.7693
41.1614-0.2225-0.43110.3528-0.0971.36460.04940.04530.12160.02550.0194-0.0099-0.10650.015-0.05980.0868-0.0040.00360.03510.00890.07969.548949.378439.8678
52.1738-0.5469-0.79520.7054-0.06891.5181-0.0907-0.0453-0.22050.0750.06950.090.2484-0.16010.0160.1729-0.0247-00.09160.01480.1119-0.949835.635745.437
60.55780.0124-0.34320.31890.17851.20060.0267-0.25220.03910.2341-0.0139-0.03270.11870.34820.00860.231-0.0107-0.01330.2331-0.01140.135219.4447.386552.1165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 48 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 74 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 145 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 259 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 260 through 294 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 295 through 335 )A0

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