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- PDB-4wwh: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (I... -

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Database: PDB / ID: 4wwh
TitleCRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM MYCOBACTERIUM SMEGMATIS (MSMEG_1704, TARGET EFI-510967) WITH BOUND D-GALACTOSE
ComponentsABC transporter
KeywordsTRANSPORT PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
: / : / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / ABC transporter
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM MYCOBACTERIUM SMEGMATIS (MSMEG_1704, TARGET EFI-510967) WITH BOUND D-GALACTOSE
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionNov 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Data collection
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 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: ABC transporter
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7395
Polymers78,2562
Non-polymers4823
Water20,5911143
1
A: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4313
Polymers39,1281
Non-polymers3022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3082
Polymers39,1281
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.045, 83.617, 100.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer

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Components

#1: Protein ABC transporter / ABC transporter sugar-binding protein


Mass: 39128.242 Da / Num. of mol.: 2 / Fragment: ABC TRANSPORTER SOLUTE BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Details: (MSE)HHHHHHSSG VDLGTENLYF QS(MSE)AEGGGGG DGDAKGTVGI A(MSE)PTKSSERW VADGQN(MSE)VDQ FKAFGYDTDL QYGDDVVQNQ VSQIEN(MSE)ITK GVKLLVIAPI DGSSLTNTLQ HAADLKIPVI SYDRLIKGTP NVDYYATFDN TKVGVLQANY ...Details: (MSE)HHHHHHSSG VDLGTENLYF QS(MSE)AEGGGGG DGDAKGTVGI A(MSE)PTKSSERW VADGQN(MSE)VDQ FKAFGYDTDL QYGDDVVQNQ VSQIEN(MSE)ITK GVKLLVIAPI DGSSLTNTLQ HAADLKIPVI SYDRLIKGTP NVDYYATFDN TKVGVLQANY IVDTLGVADG KGPFNLELFA GSPDDNNATY FFQGA(MSE)SVLQ PYIDSGKLVV KSGQTTFDQI ATLRWDGGLA QSR(MSE)DNLLSQ AYTSGRVDAV LSPYDGISRG VISALKSAGY GNAAKPLPIV TGQDAELASV KSIVAGEQTQ TVFKDTRELA KAAVQEADAV LTGGTPQVND TETYDNGVKV VPSYLLDPVS VDKSNYKKVL IDSGYYTETQ VQ
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_1704, MSMEI_1664 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QT42, monosaccharide-transporting ATPase
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1143 / 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: 1.82 Å3/Da / Density % sol: 32.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (31.9 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-galactose); Reservoir (0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30 %(w/v) PEG 4000); Cryoprotection (80% Peg3350 + 20% Reservoir

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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: Oct 20, 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: 1.2→100.24 Å / Num. obs: 176088 / % possible obs: 98.6 % / Redundancy: 13.9 % / Biso Wilson estimate: 7.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.034 / Net I/σ(I): 17.2 / Num. measured all: 2440330 / Scaling rejects: 11
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
1.2-1.229.10.8542.76704373420.7590.28884.3
6.57-100.2412.90.04757.11622512540.9990.01399.9

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→35.622 Å / FOM work R set: 0.9254 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1537 8807 5.01 %
Rwork0.1385 167151 -
obs0.1392 175958 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 43.98 Å2 / Biso mean: 11.16 Å2 / Biso min: 2.9 Å2
Refinement stepCycle: final / Resolution: 1.2→35.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 68 1143 6187
Biso mean--8.87 22.08 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085220
X-RAY DIFFRACTIONf_angle_d1.2567135
X-RAY DIFFRACTIONf_chiral_restr0.071834
X-RAY DIFFRACTIONf_plane_restr0.007938
X-RAY DIFFRACTIONf_dihedral_angle_d12.5841899
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 (%)
1.2-1.21360.27322310.22214665489683
1.2136-1.22790.21212640.21524884514888
1.2279-1.24290.22672640.21555105536991
1.2429-1.25860.21062920.20835380567296
1.2586-1.27520.20692940.188855885882100
1.2752-1.29270.19342900.174256045894100
1.2927-1.31110.19682800.167656175897100
1.3111-1.33070.1743030.162756325935100
1.3307-1.35150.19922880.159555685856100
1.3515-1.37370.17573040.154956195923100
1.3737-1.39730.19042710.15356175888100
1.3973-1.42270.16872920.144356365928100
1.4227-1.45010.16142990.14256145913100
1.4501-1.47970.17033200.140356005920100
1.4797-1.51190.16343030.133555875890100
1.5119-1.54710.14992980.128856415939100
1.5471-1.58570.16042960.127156395935100
1.5857-1.62860.13993160.120956005916100
1.6286-1.67650.15023320.122455755907100
1.6765-1.73070.14633010.125156505951100
1.7307-1.79250.1472790.125356925971100
1.7925-1.86430.14863130.124456315944100
1.8643-1.94910.143160.127656515967100
1.9491-2.05190.12632760.12356915967100
2.0519-2.18040.12722930.117956645957100
2.1804-2.34870.13143020.121557186020100
2.3487-2.5850.13162790.125457416020100
2.585-2.95890.13833010.134157466047100
2.9589-3.72730.14582970.132457986095100
3.7273-35.63750.14923130.140659986311100
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)
10.305-0.13630.05070.4667-0.05660.52960.02840.0556-0.0462-0.2262-0.00830.02340.2551-0.02-0.0280.1537-0.0192-0.02460.06950.0010.053862.898221.7185-1.0769
20.18450.1078-0.0010.38110.05070.45340.0162-0.01630.0410.03090.00830.0198-0.0222-0.0448-0.02330.0393-0.00080.00140.0508-0.00220.046363.838943.750918.4573
30.29050.0210.15520.84970.34060.69470.0255-0.025-0.00970.0395-0.00570.00060.073-0.0012-0.01970.0465-0.0015-0.00980.04720.00260.041770.786828.224416.2767
40.663-0.00110.10620.42550.1020.48380.0461-0.0029-0.07480.03280.0021-0.0240.1758-0.0602-0.02970.0764-0.0327-0.01260.07950.01730.051365.636824.009818.1198
50.6406-0.071-0.13781.32260.1860.7844-0.0046-0.00660.08350.0425-0.00260.0215-0.10570.05810.00750.0677-0.00720.00010.0631-0.00070.070666.541867.1956-4.212
60.25590.0156-0.01430.9241-0.22030.2480.0255-0.05630.06180.1576-0.00270.1027-0.11670.0252-0.02220.10160.00710.01890.0693-0.00180.071762.014463.77474.705
70.23280.024-0.12470.50530.07270.50360.00880.00870.02620.0144-0.00140.1078-0.0354-0.0644-0.01150.02830.00580.00990.04560.00250.069755.53459.4097-7.7613
80.3482-0.214-0.1460.5630.45040.86230.00160.0416-0.029-0.0928-0.00540.0221-0.02240.0212-0.01780.0599-0.0070.00020.0469-0.00420.041163.700540.367-23.6301
90.10330.14420.28031.24111.25791.4752-0.00180.0426-0.07790.0278-0.01370.05950.153-0.04310.01850.0719-0.0056-0.01010.07-0.00380.074356.074645.2583-21.8643
100.38720.1460.22350.65330.53670.79760.00280.0058-0.0320.0044-0.00920.02860.0451-0.04470.00810.047-0.0063-0.00020.0490.00210.048560.90838.2794-16.2036
110.4869-0.0305-0.03960.4050.33171.19970.0083-0.0016-0.10330.01160.0427-0.05670.18140.092-0.04540.0660.00640.00180.0541-0.00860.063370.010635.3198-16.411
120.3933-0.4625-0.34210.54440.40670.5209-0.02130.0285-0.0573-0.01560.0124-0.12690.04940.08570.00180.0430.01230.01830.0583-0.01320.081677.510838.912-18.2072
130.2832-0.0054-0.04480.50390.17720.32650.00060.02110.0242-0.05850.0052-0.0152-0.04690.0122-0.00630.0416-0.00570.00760.0473-0.00060.043668.849559.7626-16.1452
140.61750.2253-0.19790.9413-0.1820.5839-0.0113-0.00280.0229-0.0740.03790.1713-0.0194-0.0922-0.00670.03860.0088-0.00180.07490.00940.103148.997163.455-14.0498
151.1648-0.00170.1290.70430.14650.6969-0.02260.0516-0.0025-0.05060.0144-0.15750.00340.10780.01180.0764-0.01050.0230.0750.00980.080177.07861.0012-22.3363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 125 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 270 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 271 through 314 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 315 through 365 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 66 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 92 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 158 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 159 through 178 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 179 through 197 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 198 through 219 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 220 through 247 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 248 through 270 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 271 through 315 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 316 through 339 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 340 through 365 )B0

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