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- PDB-1tjb: Crystal Structure of a High Affinity Lanthanide-Binding Peptide (LBT) -

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Basic information

Entry
Database: PDB / ID: 1tjb
TitleCrystal Structure of a High Affinity Lanthanide-Binding Peptide (LBT)
ComponentsLanthanide-Binding Peptide
KeywordsDE NOVO PROTEIN / Lanthanide-Based Resonance Energy Transfer / Fluorescence / EF-Hand / Troponin Based Design / Lanthanide Binding Tag
Function / homologyTERBIUM(III) ION
Function and homology information
MethodX-RAY DIFFRACTION / SAD PHASING / Resolution: 2 Å
AuthorsNitz, M. / Sherawat, M. / Franz, K.J. / Peisach, E. / Allen, K.N. / Imperiali, B.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2004
Title: Structural Origin of the High Affinity of a Chemically Evolved Lanthanide-Binding Peptide
Authors: Nitz, M. / Sherawat, M. / Franz, K.J. / Peisach, E. / Allen, K.N. / Imperiali, B.
#1: Journal: Chembiochem / Year: 2003
Title: Lanthanide-binding tags as versatile protein coexpression probes
Authors: Franz, K.J. / Nitz, M. / Imperiali, B.
History
DepositionJun 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Lanthanide-Binding Peptide
B: Lanthanide-Binding Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3967
Polymers3,9722
Non-polymers4245
Water81145
1
A: Lanthanide-Binding Peptide
hetero molecules


  • defined by author
  • 2.25 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,2515
Polymers1,9861
Non-polymers2654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lanthanide-Binding Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1452
Polymers1,9861
Non-polymers1591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.160, 22.270, 30.030
Angle α, β, γ (deg.)90.00, 103.89, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe solution assembly is a monomer

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Components

#1: Protein/peptide Lanthanide-Binding Peptide


Mass: 1986.036 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Peptide prepared by automated solid phase peptide synthesis
#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: t-Butanol, Terbium Chloride, sodium chloride, tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 26, 2003 / Details: Osmic Mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→55 Å / Num. all: 2315 / Num. obs: 2315 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 7.8 / Num. unique all: 212 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD PHASING / Resolution: 2→17.18 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 210 -random
Rwork0.1613 ---
obs0.1647 2247 96.9 %-
all-2320 --
Displacement parametersBiso mean: 14.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 2→17.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms282 0 5 45 332
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.5
X-RAY DIFFRACTIONc_mcbond_it0.9491.5
X-RAY DIFFRACTIONc_scbond_it1.6232
X-RAY DIFFRACTIONc_mcangle_it1.3892
X-RAY DIFFRACTIONc_scangle_it2.1482.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.01-2.10.209230.1690.04426097
2.1-2.210.226270.1470.04327793.6
2.21-2.350.161290.1510.0327293.5
2.35-2.530.161250.150.03228098.2
2.53-2.780.254310.1910.04628396.9
2.78-3.190.266300.2120.04928198.6
3.19-4.010.125200.1420.02829098.3
4.01-17.180.171250.1460.03430498.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2tb.paramtb.top
X-RAY DIFFRACTION3capping.paramcapping.top
X-RAY DIFFRACTION4water_rep.paramwater_rep.top
X-RAY DIFFRACTION5ion.paramion.top

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