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- PDB-7fbb: De novo design protein D12 with MBP tag -

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Basic information

Entry
Database: PDB / ID: 7fbb
TitleDe novo design protein D12 with MBP tag
ComponentsMaltodextrin-binding protein,de novo designed protein D12
KeywordsUNKNOWN FUNCTION / DE NOVO PROTEIN
Function / homology
Function and homology information


cell envelope / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / metal ion binding
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Maltodextrin-binding protein
Similarity search - Component
Biological speciesSerratia sp. (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.307 Å
AuthorsBin, H.
CitationJournal: Nature / Year: 2022
Title: A backbone-centred energy function of neural networks for protein design.
Authors: Huang, B. / Xu, Y. / Hu, X. / Liu, Y. / Liao, S. / Zhang, J. / Huang, C. / Hong, J. / Chen, Q. / Liu, H.
History
DepositionJul 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: 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.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.pdbx_description
Revision 1.3Mar 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltodextrin-binding protein,de novo designed protein D12
B: Maltodextrin-binding protein,de novo designed protein D12


Theoretical massNumber of molelcules
Total (without water)96,0292
Polymers96,0292
Non-polymers00
Water55831
1
A: Maltodextrin-binding protein,de novo designed protein D12


Theoretical massNumber of molelcules
Total (without water)48,0151
Polymers48,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltodextrin-binding protein,de novo designed protein D12


Theoretical massNumber of molelcules
Total (without water)48,0151
Polymers48,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.078, 112.814, 84.658
Angle α, β, γ (deg.)90.000, 96.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltodextrin-binding protein,de novo designed protein D12


Mass: 48014.520 Da / Num. of mol.: 2
Mutation: D84A, K85A, E174A, N175A, K241A, E361A, K364A, D365A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. (strain FS14) (bacteria), (gene. exp.) synthetic construct (others)
Strain: FS14 / Gene: malE, JW3994 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P1LXE0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.307→67.4 Å / Num. obs: 46076 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 48.43 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.082 / Rrim(I) all: 0.217 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.31-2.436.70.6784535367270.8460.2810.7352.8100
7.29-67.470.181058315120.9620.0720.194999.8

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Processing

Software
NameVersionClassification
SCALA0.7.4data scaling
PHENIX1.1refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.307→23.906 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 2302 5.01 %
Rwork0.2253 43623 -
obs0.2272 45925 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.2 Å2 / Biso mean: 54.5923 Å2 / Biso min: 23.94 Å2
Refinement stepCycle: final / Resolution: 2.307→23.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6680 0 0 31 6711
Biso mean---40.29 -
Num. residues----879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066830
X-RAY DIFFRACTIONf_angle_d0.7419293
X-RAY DIFFRACTIONf_chiral_restr0.0471041
X-RAY DIFFRACTIONf_plane_restr0.0051202
X-RAY DIFFRACTIONf_dihedral_angle_d17.5934087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.307-2.35690.34331420.29792738100
2.3569-2.41170.31311560.28912691100
2.4117-2.47190.34451460.27782713100
2.4719-2.53870.32041550.28032713100
2.5387-2.61330.35931390.27462717100
2.6133-2.69760.30551500.27272731100
2.6976-2.79380.32751320.26842727100
2.7938-2.90550.33971550.26732724100
2.9055-3.03750.34221270.2892723100
3.0375-3.19730.33361420.27322728100
3.1973-3.39710.31711390.27312740100
3.3971-3.65850.26951240.24682756100
3.6585-4.02510.26631600.21372731100
4.0251-4.6040.21861330.1842736100
4.604-5.78690.21011620.18662732100
5.7869-23.9060.19221400.1671272397
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)
11.5133-0.745-0.0191.01220.02010.72210.0178-0.0065-0.01760.04820.01430.0390.06150.0693-0.02660.26890.0094-0.02530.308-0.0330.328721.9793-14.019833.3366
21.32250.22640.50050.8293-0.07730.4985-0.31430.2112-0.0029-0.4850.1626-0.0494-0.2129-0.21630.15350.80890.00790.02550.4701-0.09180.380715.6954-30.0691-2.7277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 446)A5 - 446
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 445)B5 - 445

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