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- PDB-4ng7: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4ng7
TitleCrystal structure of a TRAP periplasmic solute binding protein from Citrobacter koseri (CKO_04899), Target EFI-510094, apo, open structure
ComponentsTRAP periplasmic solute binding protein
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 / metal ion 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
2,3-diketo-L-gulonate TRAP transporter substrate-binding periplasmic protein
Similarity search - Component
Biological speciesCitrobacter koseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / 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
DepositionNov 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP periplasmic solute binding protein


Theoretical massNumber of molelcules
Total (without water)37,0051
Polymers37,0051
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.503, 93.503, 140.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein TRAP periplasmic solute binding protein


Mass: 37004.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter koseri (bacteria) / Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / Gene: CKO_04899 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8AR30
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 37.4 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 1 mM D-arabinoate, reservoir: 0.1 M Bis-Tris propane, pH 7, 60% v/v tacsimate, cryoprotection: 4:1 reservoir:glycerol, VAPOR DIFFUSION, ...Details: 37.4 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 1 mM D-arabinoate, reservoir: 0.1 M Bis-Tris propane, pH 7, 60% v/v tacsimate, cryoprotection: 4:1 reservoir:glycerol, 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: Aug 12, 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: 2.3→80.976 Å / Num. all: 16734 / Num. obs: 16734 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 39.21 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.4214.30.9480.83406323770.94899.9
2.42-2.5714.30.6771.13234822550.67799.9
2.57-2.7514.30.4491.73068221520.449100
2.75-2.9714.30.2722.72817819700.272100
2.97-3.2514.20.1734.32619618460.173100
3.25-3.6414.10.1086.22389016910.108100
3.64-4.2140.0966.52105615040.096100
4.2-5.1413.70.0866.61769712890.086100
5.14-7.2713.30.0747.91389210430.074100
7.27-40.48811.50.0599.370086070.05997.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N8Y

4n8y


Resolution: 2.3→40.488 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8087 / SU ML: 0.27 / σ(F): 0 / σ(I): 0 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 846 5.06 %RANDOM
Rwork0.2064 ---
all0.2087 16710 --
obs0.2087 16710 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.41 Å2 / Biso mean: 42.8384 Å2 / Biso min: 10.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 0 94 2349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082297
X-RAY DIFFRACTIONf_angle_d1.1293100
X-RAY DIFFRACTIONf_chiral_restr0.075347
X-RAY DIFFRACTIONf_plane_restr0.005400
X-RAY DIFFRACTIONf_dihedral_angle_d15.916860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.44410.33131740.257125332707100
2.4441-2.63280.27561350.234225962731100
2.6328-2.89760.2721390.228325972736100
2.8976-3.31680.28561420.218826192761100
3.3168-4.17810.25591200.185926832803100
4.1781-40.4940.20951360.19412836297299
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)
11.07350.62360.52171.63820.01561.119-0.19990.03450.46760.00950.0086-0.1996-0.47840.08120.1310.4491-0.0673-0.25320.16850.07410.55359.903137.687470.3647
22.7309-0.1289-2.12143.5664-2.0742.9777-0.35180.49650.2637-0.4797-0.1145-0.211-0.2219-0.0620.21940.4261-0.1374-0.21810.34690.11150.2588-2.437931.164656.5083
31.34480.6319-0.5131.1139-0.66081.1944-0.01930.12620.29960.0406-0.1015-0.1654-0.49450.2480.00130.3572-0.1231-0.11380.2270.15650.22291.50731.809666.0573
41.4958-0.58930.18142.8452-0.82931.86790.1122-0.55230.21850.1991-0.08050.19220.0171-0.67710.05010.2067-0.0271-0.09390.3282-0.03830.2006-12.863221.702478.4167
51.00940.22640.50051.49120.36040.9498-0.11230.2062-0.0314-0.14970.0826-0.4614-0.21720.18050.07210.2387-0.0784-0.1140.20230.08030.22325.659627.107168.007
61.4837-0.79460.81992.235-0.69591.0184-0.0566-0.07690.11180.073-0.02520.0694-0.1056-0.3438-0.04640.27080.0468-0.20710.32270.00060.2204-14.261120.148566.135
71.45720.71692.06776.60774.86388.27560.14660.2882-0.0002-0.3398-0.0905-0.1333-0.15010.0661-0.11760.5379-0.1805-0.34140.53780.29950.7707-9.602931.768550.3489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 107 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 134 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 157 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 205 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 288 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 289 through 312 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 316 through 331 )A0

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