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- PDB-5fio: DARPins as a new tool for experimental phasing in protein crystal... -

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Basic information

Entry
Database: PDB / ID: 5fio
TitleDARPins as a new tool for experimental phasing in protein crystallography
Components
  • MALTOSE-BINDING PERIPLASMIC PROTEIN
  • NI3C DARPIN MUTANT5 HG-SITE N1
KeywordsMETAL BINDING PROTEIN / DARPIN / ENGINEERED PROTEIN / EXPERIMENTAL PHASING
Function / homology
Function and homology information


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 ...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 / membrane
Similarity search - Function
Ankyrin repeat-containing 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
: / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesSYNTHETIC CONSTRUCT (others)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBatyuk, A. / Honegger, A. / Andres, F. / Briand, C. / Gruetter, M. / Plueckthun, A.
CitationJournal: To be Published
Title: Darpins as a New Tool for Experimental Phasing in Protein Crystallography
Authors: Batyuk, A. / Honegger, A. / Andres, F. / Briand, C. / Gruetter, M. / Plueckthun, A.
History
DepositionSep 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Derived calculations
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
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 / _pdbx_database_status.status_code_sf
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NI3C DARPIN MUTANT5 HG-SITE N1
B: MALTOSE-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9723
Polymers61,7722
Non-polymers2011
Water3,639202
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-6.5 kcal/mol
Surface area26190 Å2
MethodPQS
Unit cell
Length a, b, c (Å)72.610, 43.790, 82.420
Angle α, β, γ (deg.)90.00, 108.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NI3C DARPIN MUTANT5 HG-SITE N1


Mass: 18583.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DESIGNED ANKYRIN REPEAT PROTEIN WITH THREE INTERNAL REPEAT AND C-TERMINAL CAPPING REPEAT TYPE MUT5 AND ENGINEERED BURIED MERCURY BINDING SITE CYS30-CYS65 WITH BOUND HG-ION
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30SS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE
#2: Protein MALTOSE-BINDING PERIPLASMIC PROTEIN / MBP / MMBP / MALTODEXTRIN-BINDING PROTEIN


Mass: 43187.715 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-392
Source method: isolated from a genetically manipulated source
Details: INVOLVED IN THE HIGH-AFFINITY MALTOSE MEMBRANE TRANSPORT SYSTEM MALEFGK. INITIAL RECEPTOR FOR THE ACTIVE TRANSPORT OF AND CHEMOTAXIS TOWARD MALTOOLIGOSACCHARIDES.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PQE30SS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE / References: UniProt: P0AEY0, UniProt: P0AEX9*PLUS
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.14 Å3/Da / Density % sol: 42.64 % / Description: NONE
Crystal growpH: 8 / Details: 30.55% W/V PEG 6000, 0.1M TRIS-CL, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00745
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2011 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00745 Å / Relative weight: 1
ReflectionResolution: 2.1→45.18 Å / Num. obs: 28809 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.92
Reflection shellHighest resolution: 2.1 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.21 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→45.178 Å / SU ML: 0.28 / σ(F): 0.86 / Phase error: 27.46 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2525 5220 9.9 %
Rwork0.2089 --
obs0.2133 28802 93.32 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 1 202 4229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024131
X-RAY DIFFRACTIONf_angle_d0.5665613
X-RAY DIFFRACTIONf_dihedral_angle_d11.2681494
X-RAY DIFFRACTIONf_chiral_restr0.034618
X-RAY DIFFRACTIONf_plane_restr0.002733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.12410.4051630.33991525X-RAY DIFFRACTION90
2.1241-2.14910.30981740.32061573X-RAY DIFFRACTION93
2.1491-2.17530.3511770.30831632X-RAY DIFFRACTION94
2.1753-2.20280.33841680.28511534X-RAY DIFFRACTION93
2.2028-2.23180.31671680.30141550X-RAY DIFFRACTION91
2.2318-2.26240.31021590.29871438X-RAY DIFFRACTION88
2.2624-2.29470.33991790.27981643X-RAY DIFFRACTION94
2.2947-2.32890.32081770.27051584X-RAY DIFFRACTION97
2.3289-2.36530.24531770.25071598X-RAY DIFFRACTION95
2.3653-2.40410.2871850.23951647X-RAY DIFFRACTION96
2.4041-2.44560.2471800.23961614X-RAY DIFFRACTION96
2.4456-2.490.32071800.23871577X-RAY DIFFRACTION95
2.49-2.53790.28911850.24281629X-RAY DIFFRACTION96
2.5379-2.58970.25991850.24231688X-RAY DIFFRACTION96
2.5897-2.6460.3161730.2331524X-RAY DIFFRACTION94
2.646-2.70760.24591700.23861563X-RAY DIFFRACTION92
2.7076-2.77530.27531810.20261567X-RAY DIFFRACTION93
2.7753-2.85030.23231740.20871571X-RAY DIFFRACTION92
2.8503-2.93410.26491770.2211602X-RAY DIFFRACTION93
2.9341-3.02880.31171720.23711602X-RAY DIFFRACTION96
3.0288-3.13710.27081790.20931639X-RAY DIFFRACTION97
3.1371-3.26260.26771810.21451605X-RAY DIFFRACTION95
3.2626-3.41110.2641760.20761598X-RAY DIFFRACTION94
3.4111-3.59080.24531720.19041544X-RAY DIFFRACTION92
3.5908-3.81570.23461640.17711537X-RAY DIFFRACTION93
3.8157-4.11010.23161660.17331475X-RAY DIFFRACTION87
4.1101-4.52340.18831720.15641553X-RAY DIFFRACTION91
4.5234-5.17710.21171700.1631570X-RAY DIFFRACTION93
5.1771-6.51950.22921730.19581552X-RAY DIFFRACTION92
6.5195-45.1880.18141630.16731546X-RAY DIFFRACTION91
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)
19.67110.36412.91198.54233.35874.395-0.1534-1.0210.737-0.30290.17530.3688-0.7816-0.55960.11930.4994-0.0763-0.03260.4271-0.01080.1768-0.7423.3987-1.8819
23.1189-0.0709-0.21475.24750.72658.1593-0.2480.5424-0.4988-0.66550.29310.08070.51140.1706-0.06890.2741-0.03620.02080.331-0.03410.237913.588719.0352-4.1439
31.6759-1.0459-1.68392.62650.81522.0338-0.4775-0.5561-0.19540.51770.4575-0.48180.25530.9314-0.1180.28620.1790.13530.81270.05420.278229.920918.21442.7539
44.5631-0.5983-2.44210.18210.86874.51880.1583-0.4401-0.2651.0044-0.03051.21660.1648-0.3297-0.07070.7071-0.0850.38120.384-0.02310.8312-9.254337.295851.9984
51.03630.3642-0.49322.2931.51452.67540.1849-0.16370.23490.6441-0.0456-0.3217-0.14820.1577-0.09620.5259-0.0678-0.09540.25950.01380.34096.410640.315145.1516
61.575-0.17830.58342.31270.37433.3929-0.08690.03060.06210.0384-0.01660.00140.04590.07340.080.18480.0129-0.02290.15790.0380.18479.957225.181922.6505
71.41790.0976-0.57582.21360.55991.4150.0854-0.1010.04620.5524-0.17450.0054-0.26450.15560.01630.3924-0.0546-0.06660.20940.0060.25698.515433.390537.1313
89.28255.5557.80343.34534.70086.6012-0.31780.25640.078-0.5340.3071-0.0814-0.43810.13250.0420.4039-0.0502-0.03210.3050.01880.19232.812726.8292-7.0172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 11 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 50 THROUGH 101 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 102 THROUGH 170 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 7 THROUGH 42 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 43 THROUGH 118 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 119 THROUGH 245 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 246 THROUGH 372 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 33 THROUGH 49 )

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