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- PDB-4pfw: Crystal structure of mannohexaose bound oligopeptide ABC transpor... -

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Basic information

Entry
Database: PDB / ID: 4pfw
TitleCrystal structure of mannohexaose bound oligopeptide ABC transporter, periplasmic oligopeptide-binding protein (TM1226) from THERMOTOGA MARITIMA at 2.2 A resolution
ComponentsABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / oligopeptide ABC transporter / periplasmic oligopeptide-binding protein
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Mannoside ABC transport system, sugar-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.198 Å
AuthorsLu, X. / Ghimire-Rijal, S. / Cuneo, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Duplication of Genes in an ATP-binding Cassette Transport System Increases Dynamic Range While Maintaining Ligand Specificity.
Authors: Ghimire-Rijal, S. / Lu, X. / Myles, D.A. / Cuneo, M.J.
History
DepositionApr 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 5, 2014Group: Database references
Revision 2.0Sep 27, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 2.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / refine_hist / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,45714
Polymers127,6702
Non-polymers2,78712
Water9,512528
1
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2357
Polymers63,8351
Non-polymers1,3996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2237
Polymers63,8351
Non-polymers1,3886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.548, 194.227, 159.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-734-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ABC transporter substrate-binding protein / Mannoside ABC transport system / sugar-binding protein


Mass: 63835.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: THEMA_08200, Tmari_1233 / Production host: Escherichia coli (E. coli) / References: UniProt: G4FEC0
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpa1-4DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(4+1)][a-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 538 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 2.2 M AmSO4, 0.2 M tri-Li Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.198→50 Å / Num. obs: 76389 / % possible obs: 97.2 % / Redundancy: 3.9 % / Net I/σ(I): 15.7
Reflection shellResolution: 2.198→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.4 / % possible all: 97.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.198→44.862 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 3844 5.04 %
Rwork0.1643 --
obs0.167 76290 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.198→44.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8826 0 179 528 9533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089369
X-RAY DIFFRACTIONf_angle_d1.07412849
X-RAY DIFFRACTIONf_dihedral_angle_d13.5893399
X-RAY DIFFRACTIONf_chiral_restr0.0451358
X-RAY DIFFRACTIONf_plane_restr0.0061613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.198-2.22570.35421260.26372527X-RAY DIFFRACTION91
2.2257-2.2550.29921320.25292673X-RAY DIFFRACTION97
2.255-2.28590.3341560.24142626X-RAY DIFFRACTION97
2.2859-2.31860.32411470.23312674X-RAY DIFFRACTION97
2.3186-2.35320.31741370.22822620X-RAY DIFFRACTION97
2.3532-2.390.26621420.22842638X-RAY DIFFRACTION96
2.39-2.42910.28981490.21922643X-RAY DIFFRACTION96
2.4291-2.4710.25591380.20662629X-RAY DIFFRACTION96
2.471-2.51590.28811540.20452619X-RAY DIFFRACTION97
2.5159-2.56430.23481370.20352649X-RAY DIFFRACTION96
2.5643-2.61670.23981280.20132677X-RAY DIFFRACTION96
2.6167-2.67360.28081380.18992639X-RAY DIFFRACTION96
2.6736-2.73570.28811400.19412653X-RAY DIFFRACTION96
2.7357-2.80410.28411330.19072681X-RAY DIFFRACTION97
2.8041-2.880.25621480.19272642X-RAY DIFFRACTION96
2.88-2.96470.22431260.18322687X-RAY DIFFRACTION97
2.9647-3.06040.26721350.19182667X-RAY DIFFRACTION97
3.0604-3.16970.25791430.17542676X-RAY DIFFRACTION97
3.1697-3.29660.25041530.1712685X-RAY DIFFRACTION97
3.2966-3.44660.24191460.16422689X-RAY DIFFRACTION97
3.4466-3.62820.21671260.16012753X-RAY DIFFRACTION98
3.6282-3.85540.18311520.13732758X-RAY DIFFRACTION99
3.8554-4.15290.15631380.12812774X-RAY DIFFRACTION99
4.1529-4.57040.15651590.11832760X-RAY DIFFRACTION99
4.5704-5.23090.1581480.12262777X-RAY DIFFRACTION99
5.2309-6.58710.19251750.15292767X-RAY DIFFRACTION99
6.5871-44.87160.19631380.15452863X-RAY DIFFRACTION97
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)
11.56531.54160.53922.27140.00873.07310.2742-0.67780.21450.4781-0.52070.39150.2831-0.75560.23390.3421-0.17440.00510.769-0.09070.399-43.8246-51.004625.7846
22.45540.80240.79211.58050.0653.27250.4016-1.0083-0.24980.5602-0.3415-0.1160.5286-0.5369-0.03970.4751-0.2064-0.05520.67230.05590.3083-23.1471-50.096739.1087
31.69870.63381.05881.59390.91142.39310.2786-0.84710.08590.3132-0.38670.31720.2054-0.82990.07950.3195-0.14450.04580.7294-0.08220.3384-39.5322-48.363229.0064
42.546-0.8660.64889.75151.09372.18370.0601-0.1792-0.1963-0.10730.0416-0.06740.0948-0.0416-0.09230.1735-0.04640.01570.2762-0.00030.1867-30.476-60.40026.9451
52.85081.15281.44791.80451.44232.3694-0.0220.2443-0.3093-0.12670.1711-0.42730.10390.3908-0.13760.34640.0252-0.00320.31950.03160.4161-20.3515-60.68475.145
62.81711.00870.92961.64540.91111.61660.3059-0.3605-0.66490.2984-0.1393-0.29190.6207-0.1132-0.14850.4497-0.0356-0.10170.26920.11630.4352-32.1807-72.872511.3851
74.83112.45171.07155.0861-0.06953.05950.3255-0.6157-0.76080.4158-0.1291-0.99610.57620.1959-0.17120.43270.0553-0.18480.39030.09540.6155-12.1837-66.992821.2281
81.31160.2343-0.31174.18671.89021.65250.14-0.37610.2009-0.0865-0.17190.253-0.086-0.21120.02870.24260.0049-0.04550.381-0.0650.2707-33.1864-44.645315.9216
91.56120.2076-2.60185.35242.49835.75350.11120.15260.1839-0.1605-0.2206-0.4083-0.53470.03130.10530.2104-0.0559-0.05420.26330.02380.31021.5724-24.647620.9372
101.0624-1.027-0.28731.72760.73521.5736-0.1007-0.22320.16030.0486-0.1970.377-0.1904-0.59650.26950.25260.0711-0.03350.4161-0.11360.3307-21.434-25.914727.3588
113.8304-0.0721.09261.5022-0.04342.6572-0.0018-0.19830.47460.0092-0.18450.2903-0.5742-0.54790.17410.38310.1177-0.03960.3617-0.10120.3281-16.31-14.618431.1171
121.78330.4062-0.93250.8553-0.3592.9209-0.0626-0.1779-0.05610.0421-0.0626-0.18150.11020.2640.14030.21550.0426-0.0270.25710.01450.24151.4964-30.907625.0041
132.05250.009-0.18750.9398-0.20912.0549-0.08210.22350.0529-0.3219-0.0140.0825-0.0014-0.03910.11030.38720.0118-0.02240.2716-0.04540.2966-12.05-28.108-1.1667
142.8817-0.40730.65512.5943-0.12422.206-0.25850.99410.6958-0.8322-0.150.097-0.8260.2750.31060.8486-0.0238-0.07430.50860.15690.5036-6.5072-11.0473-16.2489
153.1995-0.25091.46312.51860.09133.7157-0.1470.23980.362-0.5186-0.0591-0.0833-0.4750.41880.23680.4271-0.01870.03610.25340.05760.3495-1.6391-17.4744-3.6305
162.49551.20910.44573.205-1.29642.6249-0.259-0.14340.6916-0.0281-0.0310.1357-0.7243-0.17820.3090.49510.1051-0.11830.2626-0.01560.4411-14.5459-13.3547.1053
173.49420.9332-0.98372.8113-0.85253.0152-0.0608-0.22440.7022-0.3330.04850.6568-0.5203-0.64080.02180.48280.1964-0.18450.4538-0.0850.6551-29.3177-14.47825.5683
181.20720.00271.16982.0707-1.9755.85690.0477-0.0839-0.0237-0.1607-0.0785-0.00940.10830.01650.00960.19680.02030.01230.209-0.01470.2257-8.2178-35.579614.8323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 252 )
4X-RAY DIFFRACTION4chain 'A' and (resid 253 through 301 )
5X-RAY DIFFRACTION5chain 'A' and (resid 302 through 347 )
6X-RAY DIFFRACTION6chain 'A' and (resid 348 through 466 )
7X-RAY DIFFRACTION7chain 'A' and (resid 467 through 505 )
8X-RAY DIFFRACTION8chain 'A' and (resid 506 through 560 )
9X-RAY DIFFRACTION9chain 'B' and (resid 21 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 91 )
11X-RAY DIFFRACTION11chain 'B' and (resid 92 through 189 )
12X-RAY DIFFRACTION12chain 'B' and (resid 190 through 239 )
13X-RAY DIFFRACTION13chain 'B' and (resid 240 through 347 )
14X-RAY DIFFRACTION14chain 'B' and (resid 348 through 387 )
15X-RAY DIFFRACTION15chain 'B' and (resid 388 through 424 )
16X-RAY DIFFRACTION16chain 'B' and (resid 425 through 466 )
17X-RAY DIFFRACTION17chain 'B' and (resid 467 through 505 )
18X-RAY DIFFRACTION18chain 'B' and (resid 506 through 560 )

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