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

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Basic information

Entry
Database: PDB / ID: 4mni
TitleCrystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_4736), Target EFI-510156, with bound benzoyl formate, space group P6522
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
BENZOYL-FORMIC ACID / Solute-binding protein Bpro_4736
Similarity search - Component
Biological speciesPolaromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Scott Glenn, A. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / 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
DepositionSep 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 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)37,2932
Polymers37,1421
Non-polymers1501
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.228, 107.228, 113.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

21A-577-

HOH

31A-672-

HOH

41A-751-

HOH

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Components

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


Mass: 37142.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. (bacteria) / Strain: JS666 / ATCC BAA-500 / Gene: Bpro_4736 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q122C7
#2: Chemical ChemComp-173 / BENZOYL-FORMIC ACID / OXO(PHENYL)ACETIC ACID / Phenylglyoxylic acid


Mass: 150.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 68.01 mg/mL protein in 10 mM HEPES, pH 7.5, 10 mM benzoyl formate, reservoir: MCSG2(C9) (0.2 M sodium fluoride, 20% w/v PEG 3350), cryoprotection: 4:1 reservoir:ethylene glycol, VAPOR ...Details: 68.01 mg/mL protein in 10 mM HEPES, pH 7.5, 10 mM benzoyl formate, reservoir: MCSG2(C9) (0.2 M sodium fluoride, 20% w/v PEG 3350), cryoprotection: 4:1 reservoir:ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Jul 23, 2013 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→30.95 Å / Num. all: 30901 / Num. obs: 30901 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.6 % / Biso Wilson estimate: 22.41 Å2 / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / Net I/σ(I): 16.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 21.6 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 4.9 / Num. unique all: 4413 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MNC

4mnc


Resolution: 1.9→30.877 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.8903 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 17.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 1550 5.02 %RANDOM
Rwork0.1507 ---
all0.1528 30849 --
obs0.1528 30849 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.71 Å2 / Biso mean: 33.2225 Å2 / Biso min: 8.73 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 11 292 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112527
X-RAY DIFFRACTIONf_angle_d1.2083433
X-RAY DIFFRACTIONf_chiral_restr0.069368
X-RAY DIFFRACTIONf_plane_restr0.006451
X-RAY DIFFRACTIONf_dihedral_angle_d15.342935
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.96130.20421320.17126062738
1.9613-2.03140.22691190.162426272746
2.0314-2.11270.2021350.161926252760
2.1127-2.20880.21511430.157126042747
2.2088-2.32530.20091490.146426312780
2.3253-2.47090.1781540.143826152769
2.4709-2.66160.20961420.152826372779
2.6616-2.92920.21411440.155826602804
2.9292-3.35260.20341570.156726742831
3.3526-4.22230.16581330.139327352868
4.2223-30.88130.18861420.147528853027
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)
15.10050.9052-0.9941.5231-0.77171.94390.03510.3043-0.0298-0.23340.006-0.24570.05580.154-0.03190.14610.08660.05510.2117-0.02280.140517.973750.6885-19.8849
21.91620.0222-0.18641.08960.0871.8668-0.0020.25260.0026-0.191-0.0165-0.08030.08020.06990.02520.13180.06520.03420.16220.00080.140116.056351.3997-19.0747
31.7839-0.1004-0.65821.08290.20432.4257-0.1708-0.34270.01230.19030.08180.01040.376-0.09520.07030.12840.10530.01920.1789-0.00550.13779.654748.7872-4.6641
42.25560.03710.17221.3535-0.60191.0425-0.18360.0826-0.9117-0.1192-0.12680.14251.1204-0.71490.14990.5123-0.21830.15530.3581-0.10350.4473-4.120133.8704-13.9307
51.8870.1477-0.0271.32110.27311.68610.0047-0.28880.2290.19850.0275-0.06580.18330.03860.03190.06760.078-0.00090.1734-0.02470.138612.956150.6532-7.5573
62.58690.7786-0.05281.79810.2441.7536-0.04640.12640.3522-0.2615-0.07090.2604-0.4217-0.42720.06250.11650.1007-0.01450.2211-0.03360.19974.879457.945-14.304
71.53210.2525-0.67651.11280.29290.45-0.251-0.1385-0.33430.2844-0.03550.23310.6117-0.6737-0.12210.3907-0.20010.15870.59010.00730.322-8.069640.3413-0.6101
84.03111.175-1.2611.9160.6271.21880.051-0.58380.41280.35070.02050.4040.1014-0.2749-0.04290.31820.05940.0830.47970.02620.1962.331850.7268.0611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 42 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 85 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 153 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 224 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 225 through 246 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 247 through 280 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 311 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 312 through 331 )A0

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