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- PDB-7veg: Understanding NH-pi interaction between Gln and Phe -

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Basic information

Entry
Database: PDB / ID: 7veg
TitleUnderstanding NH-pi interaction between Gln and Phe
Componentspeptide
KeywordsSTRUCTURAL PROTEIN / side chain interactions / NH-pi interaction / collagen-like peptide
Function / homologyACETYLAMINO-ACETIC ACID / (2~{S},4~{R})-4-oxidanylpyrrolidine-2-carboxamide
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.385 Å
AuthorsFan, S. / Xu, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomolecules / Year: 2022
Title: Structural Achievability of an NH-pi Interaction between Gln and Phe in a Crystal Structure of a Collagen-like Peptide.
Authors: Zhang, R. / Xu, Y. / Lan, J. / Fan, S. / Huang, J. / Xu, F.
History
DepositionSep 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / refine_ls_restr_ncs / struct_ncs_dom / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptide
B: peptide
C: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8959
Polymers6,1543
Non-polymers7426
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-5 kcal/mol
Surface area4120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.093, 28.016, 73.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein/peptide peptide


Mass: 2051.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-AAC / ACETYLAMINO-ACETIC ACID


Mass: 117.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-KLF / (2~{S},4~{R})-4-oxidanylpyrrolidine-2-carboxamide


Mass: 130.145 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H10N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 9680 / % possible obs: 98.19 % / Redundancy: 12.7 % / CC1/2: 0.994 / Net I/σ(I): 46.3
Reflection shellResolution: 1.38→1.42 Å / Num. unique obs: 9680 / CC1/2: 0.994

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YAN

5yan


Resolution: 1.385→22.89 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 968 10 %
Rwork0.1647 8712 -
obs0.1686 9680 90.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.68 Å2 / Biso mean: 18.4015 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: final / Resolution: 1.385→22.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms483 0 0 115 598
Biso mean---25.54 -
Num. residues----72
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.385-1.45770.2225590.172753540
1.4577-1.5490.271440.2045129295
1.549-1.66860.25921480.1754133199
1.6686-1.83650.21091510.17811355100
1.8365-2.10210.22041500.16691355100
2.1021-2.64770.20741560.16961394100
2.6477-22.890.17771600.1512145099

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