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- PDB-5cbn: Fusion protein of mbp3-16 and B4 domain of protein A from staphyl... -

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Basic information

Entry
Database: PDB / ID: 5cbn
TitleFusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus with chemical cross-linker EY-CBS
Components
  • Maltose-binding periplasmic protein
  • mbp3-16,Immunoglobulin G-binding protein A
KeywordsPROTEIN BINDING / Fusion / EY-CBS / alpha helix / cross-linker
Function / homology
Function and homology information


IgG binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...IgG binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / extracellular region / membrane
Similarity search - Function
Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / Ankyrin repeat-containing domain / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EYC / Maltose/maltodextrin-binding periplasmic protein / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsJeong, W.H. / Lee, H. / Song, D.H. / Lee, J.O.
CitationJournal: Nat Commun / Year: 2016
Title: Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker.
Authors: Jeong, W.H. / Lee, H. / Song, D.H. / Eom, J.H. / Kim, S.C. / Lee, H.S. / Lee, H. / Lee, J.O.
History
DepositionJul 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Maltose-binding periplasmic protein
A: mbp3-16,Immunoglobulin G-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2093
Polymers59,6872
Non-polymers5211
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.282, 75.827, 111.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 40571.961 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 31-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Antibody mbp3-16,Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A


Mass: 19115.420 Da / Num. of mol.: 1 / Fragment: B4 domain (UNP RESIDUES 218-269) / Mutation: E126A, N129A, E133C, G147A
Source method: isolated from a genetically manipulated source
Details: Fusion protein of mbp3-16 and B4 domain (UNP RESIDUES 102-153) of protein A
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Staphylococcus aureus (bacteria)
Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P38507
#3: Chemical ChemComp-EYC / 2,2'-ethyne-1,2-diylbis{5-[(chloroacetyl)amino]benzenesulfonic acid}


Mass: 521.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14Cl2N2O8S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.17 % / Description: needle-rod
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 36% w/v PEG 2000, 0.2M magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24863 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.063 / Χ2: 1.659 / Net I/av σ(I): 38.569 / Net I/σ(I): 15.5 / Num. measured all: 167724
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.386.60.50524191.55699.2
2.38-2.486.60.37424281.55599.3
2.48-2.596.70.27924411.60499.3
2.59-2.736.70.21824441.64599.6
2.73-2.96.80.1624481.799.6
2.9-3.126.90.11224751.739100
3.12-3.4470.07224951.783100
3.44-3.9370.04725121.728100
3.93-4.956.70.03925281.96499.9
4.95-506.50.02426731.30299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASER1.3.2phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX

1svx


Resolution: 2.3→42.085 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 2000 8.08 %
Rwork0.1927 --
obs0.1982 24741 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 30 113 4295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084278
X-RAY DIFFRACTIONf_angle_d1.085812
X-RAY DIFFRACTIONf_dihedral_angle_d15.6961560
X-RAY DIFFRACTIONf_chiral_restr0.039630
X-RAY DIFFRACTIONf_plane_restr0.006758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.29451380.22221575X-RAY DIFFRACTION99
2.3575-2.42130.29991410.21981589X-RAY DIFFRACTION100
2.4213-2.49250.29681390.21771585X-RAY DIFFRACTION99
2.4925-2.57290.28571400.2221601X-RAY DIFFRACTION99
2.5729-2.66490.34271410.23041603X-RAY DIFFRACTION99
2.6649-2.77160.31511410.23221603X-RAY DIFFRACTION100
2.7716-2.89770.31951410.24361602X-RAY DIFFRACTION100
2.8977-3.05040.34091440.22831640X-RAY DIFFRACTION100
3.0504-3.24140.28281400.23191590X-RAY DIFFRACTION100
3.2414-3.49160.27261440.21161640X-RAY DIFFRACTION100
3.4916-3.84280.24031450.18011645X-RAY DIFFRACTION100
3.8428-4.39830.24451440.16461646X-RAY DIFFRACTION100
4.3983-5.53940.22381480.15811671X-RAY DIFFRACTION100
5.5394-42.09210.19051540.1581751X-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)
11.6502-0.9873-0.24843.93561.40162.1340.18530.31310.0101-0.5416-0.1722-0.1234-0.03530.1351-0.05660.27810.06780.01620.28770.04830.31565.6357-2.0688-31.9572
20.12370.5872-0.91160.4738-1.85484.2222-0.0575-0.0283-0.0893-0.3229-0.0798-0.12440.62060.38290.06410.41660.08120.04460.3148-0.00590.3571-3.2606-11.138915.261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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