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- PDB-6ffl: Maltose/maltodextrin-binding domain MalE from Bdellovibrio bacter... -

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Basic information

Entry
Database: PDB / ID: 6ffl
TitleMaltose/maltodextrin-binding domain MalE from Bdellovibrio bacteriovorus bound to maltotriose
ComponentsMaltose/maltodextrin transport permease homologue
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding protein
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Bacterial extracellular solute-binding protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltotriose / : / Maltose/maltodextrin transport permease homologue
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.707 Å
AuthorsLicht, A. / Werther, T. / Bommer, M. / Neumann, K. / Schneider, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1078 Germany
CitationJournal: Res. Microbiol. / Year: 2018
Title: Structural and functional characterization of a maltose/maltodextrin ABC transporter comprising a single solute binding domain (MalE) fused to the transmembrane subunit MalF.
Authors: Licht, A. / Bommer, M. / Werther, T. / Neumann, K. / Hobe, C. / Schneider, E.
History
DepositionJan 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_sheet_hbond ...pdbx_audit_support / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _pdbx_audit_support.funding_organization / _struct_sheet_range.beg_auth_comp_id ..._pdbx_audit_support.funding_organization / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin transport permease homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9568
Polymers43,3801
Non-polymers1,5767
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-103 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.747, 106.692, 53.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Maltose/maltodextrin transport permease homologue


Mass: 43380.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: malF, Bd1227 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MNM0
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Pt
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.59 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG3350, 0.1 M BisTris pH 5.5, 0.2M LiSO4 soaked with Pt(NO3)2(NH3)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2013
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.892 Å / Relative weight: 1
ReflectionResolution: 1.707→50 Å / Num. obs: 49643 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 26.2 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.148 / Net I/σ(I): 24
Reflection shellResolution: 1.707→1.768 Å / Redundancy: 26.3 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 4807 / CC1/2: 0.906 / Rrim(I) all: 1.693 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSVERSION March 2013data reduction
XDSVERSION March 2013data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.707→47.818 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 17.22
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 2352 4.99 %random
Rwork0.1581 ---
obs0.1597 49629 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.8 Å2
Refinement stepCycle: LAST / Resolution: 1.707→47.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 44 392 3448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063243
X-RAY DIFFRACTIONf_angle_d0.8044427
X-RAY DIFFRACTIONf_dihedral_angle_d2.8252675
X-RAY DIFFRACTIONf_chiral_restr0.053491
X-RAY DIFFRACTIONf_plane_restr0.006578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7073-1.72670.28281460.29222812X-RAY DIFFRACTION94
1.7267-1.7470.28891570.26752997X-RAY DIFFRACTION100
1.747-1.76830.33361530.25482990X-RAY DIFFRACTION100
1.7683-1.79070.22431620.23853004X-RAY DIFFRACTION100
1.7907-1.81420.21471540.23072978X-RAY DIFFRACTION100
1.8142-1.83910.27881570.21943003X-RAY DIFFRACTION100
1.8391-1.86540.25641610.20963025X-RAY DIFFRACTION100
1.8654-1.89320.20641570.19252955X-RAY DIFFRACTION100
1.8932-1.92280.22791560.19392991X-RAY DIFFRACTION100
1.9228-1.95430.20471570.18252963X-RAY DIFFRACTION100
1.9543-1.9880.2171590.18223032X-RAY DIFFRACTION100
1.988-2.02420.24131550.17992968X-RAY DIFFRACTION100
2.0242-2.06310.18311630.17373002X-RAY DIFFRACTION100
2.0631-2.10520.15621570.15382994X-RAY DIFFRACTION100
2.1052-2.1510.191580.15662985X-RAY DIFFRACTION100
2.151-2.2010.23681560.15172983X-RAY DIFFRACTION100
2.201-2.25610.24751600.15453017X-RAY DIFFRACTION100
2.2561-2.31710.18421580.15873020X-RAY DIFFRACTION100
2.3171-2.38530.21271560.15582975X-RAY DIFFRACTION100
2.3853-2.46220.17971560.15122995X-RAY DIFFRACTION100
2.4622-2.55020.1941610.15363015X-RAY DIFFRACTION100
2.5502-2.65230.20011520.15842995X-RAY DIFFRACTION100
2.6523-2.7730.19651590.15582954X-RAY DIFFRACTION100
2.773-2.91920.16251620.14893016X-RAY DIFFRACTION100
2.9192-3.10210.17721560.15152988X-RAY DIFFRACTION100
3.1021-3.34150.18291530.1483002X-RAY DIFFRACTION100
3.3415-3.67770.16851630.13352984X-RAY DIFFRACTION100
3.6777-4.20960.17931540.12812989X-RAY DIFFRACTION100
4.2096-5.30260.15431560.12613022X-RAY DIFFRACTION100
5.3026-47.83720.16421510.1612985X-RAY DIFFRACTION100
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)
11.5652-0.4340.42051.8450.21321.29490.0439-0.12780.02230.2837-0.02620.4304-0.0654-0.2276-0.01510.14520.010.06570.1809-0.03930.237811.519938.566939.2617
21.715-0.94580.11462.0693-0.57321.1497-0.0202-0.13070.28460.3243-0.0598-0.1362-0.21940.08190.0780.1675-0.0257-0.02430.1463-0.03340.156627.20442.873441.8683
31.47680.48380.35652.00320.69232.24-0.03330.0404-0.2745-0.31360.01750.28730.1551-0.1493-0.00790.1773-0.0241-0.04990.1147-0.00490.203526.829212.03420.5161
41.10010.4576-0.60272.4406-0.62621.3092-0.05760.04090.0399-0.39210.03510.15530.0987-0.120.02210.14470.019-0.04990.1391-0.00810.111130.982926.465218.9067
51.0118-0.5043-0.58681.71540.90971.44760.0214-0.0645-0.01760.1848-0.08450.13810.0091-0.08890.07020.1107-0.0091-0.01040.12810.00840.115423.203330.006438.8277
60.48190.0452-0.33511.13180.06582.1210.02550.01990.00280.01570.0238-0.0764-0.03840.0082-0.030.06190.0095-0.02680.1309-0.00140.123131.120833.468727.2512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 163 )
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 229 )
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 307 )
6X-RAY DIFFRACTION6chain 'A' and (resid 308 through 385 )

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