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- PDB-7fbd: De novo design protein D53 with MBP tag -

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Basic information

Entry
Database: PDB / ID: 7fbd
TitleDe novo design protein D53 with MBP tag
ComponentsMaltodextrin-binding protein,De novo design protein D53
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 / MIR / Resolution: 2.85 Å
AuthorsBin, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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
B: Maltodextrin-binding protein,De novo design protein D53
A: Maltodextrin-binding protein,De novo design protein D53


Theoretical massNumber of molelcules
Total (without water)97,4252
Polymers97,4252
Non-polymers00
Water00
1
B: Maltodextrin-binding protein,De novo design protein D53


Theoretical massNumber of molelcules
Total (without water)48,7121
Polymers48,7121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maltodextrin-binding protein,De novo design protein D53


Theoretical massNumber of molelcules
Total (without water)48,7121
Polymers48,7121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.469, 158.469, 266.194
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Maltodextrin-binding protein,De novo design protein D53


Mass: 48712.336 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

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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: 3.33 Å3/Da / Density % sol: 63.04 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.2M Sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.605→89.03 Å / Num. obs: 29930 / % possible obs: 100 % / Redundancy: 16.8 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.506 / Rpim(I) all: 0.125 / Rrim(I) all: 0.522 / Net I/σ(I): 5.7
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
2.61-2.7513.71.5067970958200.7920.4211.5642.3100
8.24-89.0317.50.3582405613750.9760.0840.3688.999.9

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
SCALA0.7.4data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.85→13.081 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.26 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2773 1482 4.95 %
Rwork0.2284 28448 -
obs0.2308 29930 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.11 Å2 / Biso mean: 33.0972 Å2 / Biso min: 13.91 Å2
Refinement stepCycle: final / Resolution: 2.85→13.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6747 0 0 0 6747
Num. residues----894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016901
X-RAY DIFFRACTIONf_angle_d0.979388
X-RAY DIFFRACTIONf_chiral_restr0.0571039
X-RAY DIFFRACTIONf_plane_restr0.0071224
X-RAY DIFFRACTIONf_dihedral_angle_d18.7214106
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.85-2.9410.37191350.31272576
2.941-3.04490.35271450.29362545
3.0449-3.16510.32421260.26892577
3.1651-3.3070.33391480.26232539
3.307-3.47820.30981310.26092560
3.4782-3.69150.28981390.24942574
3.6915-3.96920.30231170.23762607
3.9692-4.35510.25261210.20432595
4.3551-4.95510.26831360.17962598
4.9551-6.13390.22851410.21012609
6.1339-13.0810.17491430.17032668
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)
10.5952-0.01490.23460.55350.53571.4460.0115-0.03750.17360.0374-0.18840.29350.067-0.72950.17040.3063-0.26220.03260.6546-0.10540.367728.913211.549784.7593
21.10120.39570.14070.89880.24550.8772-0.03330.22180.04770.13240.098-0.1230.2088-0.0111-0.03540.1596-0.0439-0.01450.17190.01550.215776.595214.675955.5442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 2 through 445)B2 - 445
2X-RAY DIFFRACTION2(chain 'A' and resid 2 through 451)A2 - 451

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