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

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Basic information

Entry
Database: PDB / ID: 4mev
TitleCrystal structure of a TRAP periplasmic solute binding protein from Rhodoferax ferrireducens (Rfer_1840), Target EFI-510211, with bound malonate, space group I422
ComponentsTRAP dicarboxylate transporter-DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP periplasmic solute binding family / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


organic substance transport / transmembrane transport / periplasmic space
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
CITRIC ACID / MALONATE ION / Solute-binding protein Rfer_1840
Similarity search - Component
Biological speciesRhodoferax ferrireducens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Zhao, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Zhao, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / 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
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)38,1163
Polymers37,8221
Non-polymers2942
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.947, 129.947, 104.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

21A-653-

HOH

31A-782-

HOH

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Components

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


Mass: 37821.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodoferax ferrireducens (bacteria) / Strain: T118 / Gene: Rfer_1840 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q21XD7
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: 50 mg/mL protein in 10 mM HEPES, pH 7.5, 10 mM malonate, reservoir (MCSG4 C1): 0.1 M Bis-Tris Propane, pH 7.0, 2 M diammonium hydrogen citrate, cryoprotection: 4:1 2.5 M diammonium hydrogen ...Details: 50 mg/mL protein in 10 mM HEPES, pH 7.5, 10 mM malonate, reservoir (MCSG4 C1): 0.1 M Bis-Tris Propane, pH 7.0, 2 M diammonium hydrogen citrate, cryoprotection: 4:1 2.5 M diammonium hydrogen citrate:reservoir, VAPOR DIFFUSION, SITTING DROP

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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: Aug 23, 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: 1.8→100 Å / Num. all: 41044 / Num. obs: 41044 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Χ2: 0.939 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.834.50.65820580.7391100
1.83-1.864.60.59620221.1151100
1.86-1.94.70.48520370.7851100
1.9-1.944.70.39820640.9931100
1.94-1.984.80.35620320.8271100
1.98-2.034.80.29820540.8911100
2.03-2.084.80.27920461.113199.9
2.08-2.134.90.22920550.971199.9
2.13-2.24.90.20520350.998199.9
2.2-2.274.90.19720521.297199.7
2.27-2.3550.16420601.027199.9
2.35-2.4450.13720361.029199.6
2.44-2.5550.11720661.01199.4
2.55-2.695.10.10620521.049199.3
2.69-2.865.10.08720560.977199.2
2.86-3.085.10.07320580.951198.6
3.08-3.395.10.05720530.9198.5
3.39-3.885.10.04820541.013197.7
3.88-4.895.10.03520610.658196.9
4.89-10050.02720930.443193.1

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Processing

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

4mco


Resolution: 1.8→23.509 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8976 / SU ML: 0.16 / σ(F): 0 / σ(I): 0 / Phase error: 16.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.172 1988 4.92 %RANDOM
Rwork0.1428 ---
all0.1443 40419 --
obs0.1443 40419 97.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.25 Å2 / Biso mean: 25.9372 Å2 / Biso min: 10.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 20 340 2740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012473
X-RAY DIFFRACTIONf_angle_d1.2593331
X-RAY DIFFRACTIONf_chiral_restr0.07363
X-RAY DIFFRACTIONf_plane_restr0.006428
X-RAY DIFFRACTIONf_dihedral_angle_d14.177935
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84520.27021080.21972492260089
1.8452-1.89510.23731310.19532597272893
1.8951-1.95080.23381360.18242681281796
1.9508-2.01380.19181550.158727482903100
2.0138-2.08570.18111420.15327832925100
2.0857-2.16920.19621420.140227872929100
2.1692-2.26780.2111460.159327812927100
2.2678-2.38730.15391490.13927782927100
2.3873-2.53670.17591500.129827732923100
2.5367-2.73220.18711260.13812812293899
2.7322-3.00670.16351550.14312778293399
3.0067-3.44060.14511450.13942793293898
3.4406-4.33040.13371470.11662792293997
4.3304-23.51120.17411560.14192836299295
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)
11.09640.4155-0.14311.6659-0.34411.3262-0.0157-0.0899-0.0718-0.0058-0.0521-0.06290.1847-0.01270.06010.1223-0.01020.03220.11950.01750.113345.578741.541223.2807
20.9802-0.25330.08251.7522-0.67111.96540.0606-0.0040.073-0.05730.00640.2004-0.0881-0.2975-0.06270.1006-0.01160.02020.15160.01420.146534.881555.970214.6737
30.954-0.23530.07951.2685-0.5891.22960.0354-0.0794-0.0928-0.08740.07090.26270.1436-0.3306-0.10090.1319-0.04190.01220.16480.01050.170934.268547.175917.1453
44.0183-1.60452.17992.0265-1.20313.42190.20250.2285-0.2002-0.3562-0.1367-0.01320.44360.1891-0.03270.2137-0.02950.05960.10040.00830.154346.21137.852812.7235
51.19820.6458-0.79483.477-0.1292.60570.01210.19930.1211-0.29590.11380.1896-0.1723-0.0176-0.11750.12740.0504-0.00090.15570.03140.175236.309759.55454.4928
63.7217-0.9973-0.53633.52210.29915.453-0.0158-0.09390.12350.0929-0.0485-0.1401-0.07320.10280.05620.1318-0.01460.0160.07620.00510.179150.45963.407420.2871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 142 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 187 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 257 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 258 through 292 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 293 through 314 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 315 through 338 )A0

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