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- PDB-4nx1: Crystal structure of a trap periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4nx1
TitleCrystal structure of a trap periplasmic solute binding protein from Sulfitobacter sp. nas-14.1, target EFI-510292, with bound alpha-D-taluronate
ComponentsC4-dicarboxylate transport system substrate-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
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
alpha-D-talopyranuronic acid / Solute-binding protein NAS141_03721
Similarity search - Component
Biological speciesSulfitobacter sp. NAS-14.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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
DepositionDec 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C4-dicarboxylate transport system substrate-binding protein
B: C4-dicarboxylate transport system substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6194
Polymers73,2312
Non-polymers3882
Water14,358797
1
A: C4-dicarboxylate transport system substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8102
Polymers36,6151
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C4-dicarboxylate transport system substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8102
Polymers36,6151
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.523, 82.425, 106.815
Angle α, β, γ (deg.)90.000, 140.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein C4-dicarboxylate transport system substrate-binding protein


Mass: 36615.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfitobacter sp. NAS-14.1 (bacteria) / Strain: sp. NAS-14.1 / Gene: NAS141_03721 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3T0D1
#2: Sugar ChemComp-X1X / alpha-D-talopyranuronic acid / alpha-D-taluronic acid / D-taluronic acid / taluronic acid / alpha-D-taluronate


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DTalpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-talopyranuronic acidCOMMON NAMEGMML 1.0
a-D-TalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
TalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (32.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Taluronate); Reservoir (0.1 M Tris Hydrochloride pH 8.5, 1.2 M tri-Sodium Citrate Dihydrate); Cryoprotection (1.6 M Na3Citrate), ...Details: Protein (32.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Taluronate); Reservoir (0.1 M Tris Hydrochloride pH 8.5, 1.2 M tri-Sodium Citrate Dihydrate); Cryoprotection (1.6 M Na3Citrate), 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 MX-225 / Detector: CCD / Date: Nov 20, 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: 1.6→32.55 Å / Num. all: 93292 / Num. obs: 93292 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 18.99 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 11.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 2.2 / Num. unique all: 13576 / Rsym value: 0.811 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXAUTSOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→27.159 Å / Occupancy max: 1 / Occupancy min: 0.64 / FOM work R set: 0.9016 / SU ML: 0.16 / σ(F): 0 / σ(I): 0 / Phase error: 17.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 4675 5.01 %RANDOM
Rwork0.1525 ---
obs0.1537 93281 99.78 %-
all-93281 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.63 Å2 / Biso mean: 27.8729 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 26 797 5550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014839
X-RAY DIFFRACTIONf_angle_d1.2896559
X-RAY DIFFRACTIONf_chiral_restr0.078754
X-RAY DIFFRACTIONf_plane_restr0.007859
X-RAY DIFFRACTIONf_dihedral_angle_d13.0211820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.29131750.25882921309699
1.6182-1.63720.28361430.244929263069100
1.6372-1.65720.22791530.230629383091100
1.6572-1.67810.23751390.220829823121100
1.6781-1.70020.25641400.211829473087100
1.7002-1.72350.25861480.202929843132100
1.7235-1.74810.23311470.19129513098100
1.7481-1.77420.23821720.193529003072100
1.7742-1.80190.20321790.182629463125100
1.8019-1.83150.20791480.174829553103100
1.8315-1.8630.18981630.162429283091100
1.863-1.89690.21031500.159929953145100
1.8969-1.93340.17271480.155929063054100
1.9334-1.97280.17821560.15729683124100
1.9728-2.01570.1921700.148629283098100
2.0157-2.06260.18281460.143329883134100
2.0626-2.11420.18791520.139429873139100
2.1142-2.17130.16691670.137629423109100
2.1713-2.23520.15061520.136629403092100
2.2352-2.30730.19441460.133829453091100
2.3073-2.38970.17351620.136729513113100
2.3897-2.48530.161550.137529793134100
2.4853-2.59830.17281460.147829633109100
2.5983-2.73520.18361930.153829413134100
2.7352-2.90640.19971340.15629713105100
2.9064-3.13050.18171540.168329743128100
3.1305-3.4450.20491420.153830103152100
3.445-3.94220.14671770.134229483125100
3.9422-4.96180.12081610.114129873148100
4.9618-27.16320.16641570.16732905306295
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)
13.60770.5704-1.21430.94990.33460.7706-0.06440.5491-0.1894-0.4363-0.1119-0.06390.12670.12190.17510.22420.05980.01130.27990.02440.156831.093831.05444.1017
22.05250.7246-0.62441.8632-0.25471.5245-0.09650.64650.1249-0.57420.0382-0.0849-0.1455-0.00850.0460.25190.02350.01170.27880.04080.146931.233438.589940.8047
31.1608-0.2727-0.61141.0723-0.12180.6032-0.0122-0.0582-0.1293-0.0779-0.0719-0.04050.06020.16510.07860.13650.01820.0050.17020.04150.174533.931829.962854.954
40.87030.03830.28320.6683-0.3552.34170.03650.00130.3144-0.0876-0.1932-0.2286-0.70050.12870.10130.22030.03-0.03510.19920.01090.226826.447541.071767.3926
52.1753-1.4493-0.06550.9713-0.09320.9695-0.33140.06871.34610.20670.0003-0.3871-0.61090.14540.18580.3367-0.0203-0.11580.19490.04020.452830.120147.432361.7031
61.5245-0.45950.24590.8889-0.21081.2515-0.0077-0.1758-0.2610.02710.02770.23910.0541-0.13640.01090.10660.00970.00090.14950.04560.21918.743128.46366.4892
71.5913-0.0015-0.28611.418-0.37791.18130.0007-0.0099-0.178-0.1451-0.04820.1289-0.0231-0.02580.02160.11360.0248-0.03080.10820.03120.152724.115934.355257.1028
82.54270.3659-0.57520.6979-0.09290.75590.1010.1933-0.0282-0.1622-0.07550.1439-0.1285-0.0921-0.02560.19090.0497-0.03960.18230.04260.182720.411941.161249.4172
91.76390.56171.15161.37170.08091.735-0.3349-0.44520.52420.32770.01510.5733-0.5217-0.32940.27680.31270.0724-0.0460.2906-0.06010.38817.845340.864473.5945
100.8506-0.4288-0.4481.27630.00481.4460.02690.2922-0.2217-0.2342-0.030.40770.1485-0.4233-0.03270.1887-0.0102-0.05420.2866-0.0470.2379-23.638952.378543.0975
111.3666-0.2177-0.28051.08340.3161.08790.0046-0.0931-0.06480.0360.0604-0.03880.04870.0848-0.0650.16770.0341-0.00150.1484-0.00880.1266-7.377254.03150.5494
121.49640.0928-0.14771.1257-0.13951.70.0514-0.0230.2243-0.1775-0.0574-0.1252-0.32830.1302-0.01570.2398-0.00520.03530.1578-0.01540.17122.201968.828646.906
130.85640.03090.28471.41490.2821.02110.02330.11630.0861-0.3086-0.01480.0707-0.1302-0.0296-0.0120.20550.0628-0.00720.1396-0.01120.078-9.500761.163540.706
142.46030.4886-1.5511.3095-0.45072.4225-0.02170.1601-0.3565-0.2684-0.02490.09630.2799-0.07320.03450.25740.0247-0.01740.1543-0.04670.1747-11.58146.344339.0981
150.4195-0.05040.30020.75990.23011.82940.09160.0498-0.0011-0.15460.0231-0.32020.16850.6287-0.12010.20080.05630.01590.2662-0.04840.22576.737157.047850.3241
161.7819-0.3805-0.96570.29490.310.5739-0.06030.09570.4341-0.21770.37650.1786-0.1868-0.26450.1750.65510.1828-0.11220.3476-0.00430.34748.619432.433738.3853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 41 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 67 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 99 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 116 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 140 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 141 through 221 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 253 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 254 through 289 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 290 through 328 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 29 through 84 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 85 through 163 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 164 through 195 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 196 through 253 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 254 through 289 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 290 through 330 )B0
16X-RAY DIFFRACTION16chain 'A' and (resid 6 through 11)A0

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