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- PDB-7jrh: X-ray crystal structure of a cyclic peptide containing medin(19-2... -

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Basic information

Entry
Database: PDB / ID: 7jrh
TitleX-ray crystal structure of a cyclic peptide containing medin(19-25) and medin(31-37)
ComponentsCyclic peptide ASP-GLN-TRP-MLE-GLN-VAL-ASP-ORD-GLU-VAL-THR-GLY-ILE-ILE-THR-ORD
KeywordsDE NOVO PROTEIN / medin / cyclic / hairpin / MOF / framework
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.32 Å
AuthorsWierzbicki, M. / Howitz, W.J. / Nowick, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
National Science Foundation (NSF, United States)CHE1808096 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Interpenetrating Cubes in the X-ray Crystallographic Structure of a Peptide Derived from Medin 19-36 .
Authors: Howitz, W.J. / Wierzbicki, M. / Cabanela, R.W. / Saliba, C. / Motavalli, A. / Tran, N. / Nowick, J.S.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic peptide ASP-GLN-TRP-MLE-GLN-VAL-ASP-ORD-GLU-VAL-THR-GLY-ILE-ILE-THR-ORD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9393
Polymers1,8591
Non-polymers802
Water19811
1
A: Cyclic peptide ASP-GLN-TRP-MLE-GLN-VAL-ASP-ORD-GLU-VAL-THR-GLY-ILE-ILE-THR-ORD
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)23,27136
Polymers22,30912
Non-polymers96224
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_654-x+1,y,-z-11
crystal symmetry operation4_544x,-y-1,-z-11
crystal symmetry operation5_645z+1,x-1,y1
crystal symmetry operation6_654z+1,-x,-y-11
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_544-z,x-1,-y-11
crystal symmetry operation9_654y+1,z,x-11
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_645y+1,-z-1,-x1
crystal symmetry operation12_544-y,-z-1,x-11
Buried area4400 Å2
ΔGint-121 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.486, 42.486, 42.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-101-

CA

21A-102-

CA

31A-207-

HOH

41A-208-

HOH

51A-209-

HOH

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Components

#1: Protein/peptide Cyclic peptide ASP-GLN-TRP-MLE-GLN-VAL-ASP-ORD-GLU-VAL-THR-GLY-ILE-ILE-THR-ORD


Mass: 1859.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.73 Å3/Da / Density % sol: 28.77 % / Description: cube
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NaOAc, 0.02M CaCl2, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.32→30.09 Å / Num. obs: 51865 / % possible obs: 99.74 % / Redundancy: 16.6 % / Biso Wilson estimate: 15.04 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04568 / Rpim(I) all: 0.008085 / Rrim(I) all: 0.04648 / Net I/σ(I): 30.81
Reflection shellResolution: 1.321→1.368 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.3153 / Mean I/σ(I) obs: 3.32 / Num. unique obs: 2021 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.1275 / Rrim(I) all: 0.3423 / % possible all: 97.83

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Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
SAINTdata reduction
SADABSdata scaling
AutoSolphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.32→30.04 Å / SU ML: 0.075 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 37.4445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2103 315 9.99 %
Rwork0.1772 5233 -
obs0.1808 3117 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.59 Å2
Refinement stepCycle: LAST / Resolution: 1.32→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms130 0 2 11 143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092131
X-RAY DIFFRACTIONf_angle_d1.5117178
X-RAY DIFFRACTIONf_chiral_restr0.091321
X-RAY DIFFRACTIONf_plane_restr0.005822
X-RAY DIFFRACTIONf_dihedral_angle_d35.968233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.450.26251500.29831258X-RAY DIFFRACTION97.24
1.45-1.660.3081300.26431352X-RAY DIFFRACTION100
1.66-2.090.231540.20341296X-RAY DIFFRACTION100
2.1-30.040.17911470.13691327X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.62816389748 Å / Origin y: -5.84557566007 Å / Origin z: -19.9504909138 Å
111213212223313233
T0.120345903853 Å2-0.0199735133909 Å2-0.000137554456755 Å2-0.129330736713 Å20.0289755494964 Å2--0.147444159995 Å2
L0.851092165584 °2-0.21535012062 °20.060723544152 °2-1.02273554412 °20.85431009085 °2--3.04294435672 °2
S0.0444540216943 Å °0.0610179989821 Å °-0.121627598276 Å °-0.0994899229761 Å °-0.00384850915064 Å °-0.168571432922 Å °0.0214374728934 Å °-0.048077593414 Å °-0.136710607131 Å °
Refinement TLS groupSelection details: all

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