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- PDB-3t4f: Crystal Structure of a KGE Collagen Mimetic Peptide at 1.68 A -

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Entry
Database: PDB / ID: 3t4f
TitleCrystal Structure of a KGE Collagen Mimetic Peptide at 1.68 A
Componentscollagen mimetic peptide
KeywordsBIOSYNTHETIC PROTEIN / collagen mimetic peptide / Triple Helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsFallas, J.A. / Dong, J. / Miller, M.D. / Tao, Y.J. / Hartgerink, J.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-0645474 United States
Robert A. Welch FoundationC1557 United States
Robert A. Welch FoundationC1565 United States
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural insights into charge pair interactions in triple helical collagen-like proteins.
Authors: Fallas, J.A. / Dong, J. / Tao, Y.J. / Hartgerink, J.D.
#1: Journal: Biomacromolecules / Year: 2020
Title: Covalent Capture of Collagen Triple Helices Using Lysine-Aspartate and Lysine-Glutamate Pairs
Authors: Hulgan, S.A.H. / Jalan, A.A. / Li, I.C. / Walker, D.R. / Miller, M.D. / Kosgei, A.J. / Xu, W. / Phillips, G.N. / Hartgerink, J.D.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 2.0Sep 2, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / audit_author / chem_comp / citation / citation_author / diffrn / diffrn_radiation / entity / entity_poly / entity_poly_seq / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_conn / struct_keywords / struct_ref / struct_ref_seq
Item: _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] ..._atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][3] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _diffrn_radiation.monochromator / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.SG_entry / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_mod_residue.label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _reflns.d_resolution_low / _reflns.number_all / _reflns.number_obs / _reflns.observed_criterion_sigma_F / _reflns.observed_criterion_sigma_I / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _software.classification / _software.name / _software.version / _struct.pdbx_CASP_flag / _struct.title / _struct_keywords.text / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Description: Sequence discrepancy
Details: modeled the N-Terminal Acetylation and C-Terminal Amidation
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: collagen mimetic peptide
B: collagen mimetic peptide
C: collagen mimetic peptide
D: collagen mimetic peptide
E: collagen mimetic peptide
F: collagen mimetic peptide


Theoretical massNumber of molelcules
Total (without water)13,3706
Polymers13,3706
Non-polymers00
Water4,612256
1
A: collagen mimetic peptide
B: collagen mimetic peptide
C: collagen mimetic peptide


Theoretical massNumber of molelcules
Total (without water)6,6853
Polymers6,6853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-23 kcal/mol
Surface area4620 Å2
MethodPISA
2
D: collagen mimetic peptide
E: collagen mimetic peptide
F: collagen mimetic peptide


Theoretical massNumber of molelcules
Total (without water)6,6853
Polymers6,6853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-22 kcal/mol
Surface area4440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)14.026, 23.815, 67.657
Angle α, β, γ (deg.)95.010, 94.690, 94.860
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
collagen mimetic peptide


Mass: 2228.375 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: Fmoc Solid Phase Peptide Chemistry with N-Terminal Acetylation and C-Terminal Amidation
Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.69 Å3/Da / Density % sol: 27.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 50% Tacsimate buffer, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 8, 2011
RadiationMonochromator: Osmic multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.68→18.51 Å / Num. obs: 7978 / % possible obs: 80.1 % / Redundancy: 1.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.4
Reflection shellResolution: 1.68→1.74 Å / Rmerge(I) obs: 0.12 / Num. unique obs: 756 / % possible all: 76.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
CrystalCleardata collection
EPMRphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QSU

1qsu


Resolution: 1.68→18.51 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 15.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1413 392 4.92 %RANDOM
Rwork0.1013 7577 --
obs0.1033 7969 80.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.78 Å2 / Biso mean: 13.7051 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: final / Resolution: 1.68→18.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 0 263 1217
Biso mean---16.55 -
Num. residues----156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081072
X-RAY DIFFRACTIONf_angle_d1.2151505
X-RAY DIFFRACTIONf_chiral_restr0.052142
X-RAY DIFFRACTIONf_plane_restr0.006215
X-RAY DIFFRACTIONf_dihedral_angle_d9.363564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.920.19881250.12352445257079
1.92-2.420.13421240.09482541266581
2.42-18.510.12821430.09812591273484

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