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- PDB-7fbc: De novo design protein D22 with MBP tag -

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Basic information

Entry
Database: PDB / ID: 7fbc
TitleDe novo design protein D22 with MBP tag
ComponentsMaltodextrin-binding protein,De novo design protein D22
KeywordsUNKNOWN FUNCTION / DE NOVO PROTEIN
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space
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
Similarity search - Domain/homology
Maltodextrin-binding protein
Similarity search - Component
Biological speciesSerratia sp. (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.85 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

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein,De novo design protein D22


Theoretical massNumber of molelcules
Total (without water)49,8661
Polymers49,8661
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20660 Å2
Unit cell
Length a, b, c (Å)61.629, 77.137, 94.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltodextrin-binding protein,De novo design protein D22


Mass: 49865.621 Da / Num. of mol.: 1 / 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.: 116 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
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: 7.24 / Details: 50% v/v PEG 500 MME, 0.1M Sodium HEPES, pH 7.24

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.74→48.149 Å / Num. obs: 39308 / % possible obs: 99.6 % / Redundancy: 4.117 % / Biso Wilson estimate: 22.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.096 / Χ2: 0.818 / Net I/σ(I): 10.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.74-1.853.8581.0411.575429114303140740.561.20598.4
1.85-1.984.2850.63.135750713420134190.8260.685100
1.98-2.144.1420.3285.275183812520125150.9280.375100
2.14-2.344.1370.1918.284742411474114640.9720.21999.9
2.34-2.624.2840.12212.024453310406103940.9870.13999.9
2.62-3.024.0710.08416.0437290918691600.9910.09699.7
3.02-3.694.20.06221.4532616777677660.9940.07199.9
3.69-5.213.9830.05125.2223785600159710.9960.05899.5
5.21-48.0694.0210.04625.9313367334833240.9970.05399.3

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
SCALA0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 1.85→48.069 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.77 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.215 1939 4.93 %
Rwork0.1843 37369 -
obs0.1858 39308 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.45 Å2 / Biso mean: 28.657 Å2 / Biso min: 10.11 Å2
Refinement stepCycle: final / Resolution: 1.85→48.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 0 116 3612
Biso mean---24.42 -
Num. residues----461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093573
X-RAY DIFFRACTIONf_angle_d0.8924860
X-RAY DIFFRACTIONf_chiral_restr0.057543
X-RAY DIFFRACTIONf_plane_restr0.007633
X-RAY DIFFRACTIONf_dihedral_angle_d17.0222139
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.85-1.89630.2781450.20912622
1.8963-1.94750.21151360.18192632
1.9475-2.00480.21381470.17722602
2.0048-2.06960.22351280.18242658
2.0696-2.14350.22191340.17592649
2.1435-2.22940.21841350.17622628
2.2294-2.33080.2181390.18162643
2.3308-2.45370.22981280.18692678
2.4537-2.60740.21681320.19282647
2.6074-2.80870.21191370.1952688
2.8087-3.09130.26671510.2072655
3.0913-3.53850.22081260.19562711
3.5385-4.45770.18231360.16672727
4.4577-48.0690.19741650.17632829
Refinement TLS params.Method: refined / Origin x: 12.9131 Å / Origin y: 10.2768 Å / Origin z: 7.5697 Å
111213212223313233
T0.1314 Å2-0.0001 Å20.0051 Å2-0.1144 Å2-0.0103 Å2--0.1576 Å2
L0.6378 °20.0661 °20.1606 °2-0.2663 °2-0.0328 °2--1.12 °2
S-0.0181 Å °-0.0214 Å °-0.0981 Å °0.0057 Å °-0.0157 Å °0.0052 Å °0.1737 Å °0.0027 Å °0.0416 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 2 through 462)

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