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- PDB-4jw3: Selection of specific protein binders for pre-defined targets fro... -

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Basic information

Entry
Database: PDB / ID: 4jw3
TitleSelection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep)
Components
  • Alpha-helical artificial proteins
  • Neocarzinostatin
KeywordsDNA binding protein/de novo protein / alpha-helical protein / Protein engineered to interact with protein of interest / NCS 3tes24 variant / DNA binding protein-de novo protein complex
Function / homology
Function and homology information


defense response to bacterium / DNA binding
Similarity search - Function
Neocarzinostatin-like / Neocarzinostatin family / Neocarzinostatin family / Neocarzinostatin-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStreptomyces malayensis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGuellouz, A. / Valerio-Lepiniec, M. / Urvoas, A. / Chevrel, A. / Graille, M. / Fourati-Kammoun, Z. / Desmadril, M. / van Tilbeurgh, H. / Minard, P.
CitationJournal: Plos One / Year: 2013
Title: Selection of Specific Protein Binders for Pre-Defined Targets from an Optimized Library of Artificial Helicoidal Repeat Proteins (alphaRep).
Authors: Guellouz, A. / Valerio-Lepiniec, M. / Urvoas, A. / Chevrel, A. / Graille, M. / Fourati-Kammoun, Z. / Desmadril, M. / van Tilbeurgh, H. / Minard, P.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neocarzinostatin
B: Neocarzinostatin
C: Alpha-helical artificial proteins
D: Alpha-helical artificial proteins


Theoretical massNumber of molelcules
Total (without water)55,3804
Polymers55,3804
Non-polymers00
Water1086
1
A: Neocarzinostatin
C: Alpha-helical artificial proteins


Theoretical massNumber of molelcules
Total (without water)27,6902
Polymers27,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-8 kcal/mol
Surface area10150 Å2
MethodPISA
2
B: Neocarzinostatin
D: Alpha-helical artificial proteins


Theoretical massNumber of molelcules
Total (without water)27,6902
Polymers27,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.210, 59.210, 65.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Neocarzinostatin / NCS / Mitomalcin / MMC


Mass: 12196.199 Da / Num. of mol.: 2 / Mutation: D33W G35A, C37W, W39R, L45W, C47Y, F52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces malayensis (bacteria) / Gene: ncsA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3S0
#2: Protein Alpha-helical artificial proteins


Mass: 15493.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3,350; 0.2 M MgCl2; 0.1 M BisTris , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 14697 / Num. obs: 14080 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 72.53 Å2 / Rsym value: 0.057 / Net I/σ(I): 15.7
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.55 / % possible all: 96.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LTM, 4JW2

3ltm

4jw2


Resolution: 2.6→33.77 Å / Cor.coef. Fo:Fc: 0.9088 / Cor.coef. Fo:Fc free: 0.8715 / SU R Cruickshank DPI: 0.803 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 704 5.01 %RANDOM
Rwork0.2238 ---
all0.2258 14697 --
obs0.2258 14054 95.48 %-
Displacement parametersBiso mean: 76.68 Å2
Baniso -1Baniso -2Baniso -3
1--8.0221 Å20 Å20 Å2
2---15.3707 Å20 Å2
3---23.3928 Å2
Refine analyzeLuzzati coordinate error obs: 0.487 Å
Refinement stepCycle: LAST / Resolution: 2.6→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 0 6 3095
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013150HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124285HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1038SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes475HARMONIC5
X-RAY DIFFRACTIONt_it3150HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion20.55
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3471SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.81 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2862 139 5 %
Rwork0.2349 2640 -
all0.2375 2779 -
obs--95.48 %
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)
14.2325-1.8549-0.85612.7730.63382.48460.08260.0406-0.0652-0.38040.03180.3302-0.34380.0083-0.11430.12660.0348-0.108-0.11580.016-0.178415.505620.01229.8423
23.97630.32550.38013.233-0.24883.2391-0.1069-0.5227-0.49840.15140.27040.54420.4102-0.1946-0.16350.05310.10030.0025-0.11340.1018-0.146315.7820.165122.2476
31.62240.1541-1.79563.2376-1.55162.38530.0571-0.13930.32070.0208-0.2035-0.5442-0.34980.54420.14650.0968-0.1153-0.0760.0588-0.0249-0.2136.338225.167212.5302
41.37740.36080.76992.9949-1.34642.21590.0867-0.1232-0.336-0.1391-0.2387-0.49270.38230.53880.1520.05250.1520.03540.07390.0299-0.182737.1898-3.602920.304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|112 }A2 - 112
2X-RAY DIFFRACTION2{ B|3 - B|114 }B3 - 114
3X-RAY DIFFRACTION3{ C|8 - C|104 }C8 - 104
4X-RAY DIFFRACTION4{ D|9 - D|104 }D9 - 104

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