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- PDB-3h5f: Switching the Chirality of the Metal Environment Alters the Coord... -

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Basic information

Entry
Database: PDB / ID: 3h5f
TitleSwitching the Chirality of the Metal Environment Alters the Coordination Mode in Designed Peptides.
ComponentsCOIL SER L16L-Pen
KeywordsDE NOVO PROTEIN / DE-NOVO PROTEIN / PARALLEL THREE-STRANDED COILED COIL / L-PENICILLAMINE
Function / homologyACETATE ION
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsPeacock, A.F.A. / Stuckey, J.A. / Pecoraro, V.L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Switching the Chirality of the Metal Environment Alters the Coordination Mode in Designed Peptides.
Authors: Peacock, A.F. / Stuckey, J.A. / Pecoraro, V.L.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3May 4, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COIL SER L16L-Pen
B: COIL SER L16L-Pen
C: COIL SER L16L-Pen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,48911
Polymers10,0623
Non-polymers4278
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.827, 29.244, 44.460
Angle α, β, γ (deg.)90.000, 118.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-31-

CL

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Components

#1: Protein/peptide COIL SER L16L-Pen


Mass: 3353.903 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Synthetic construct
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 200 mM MgCl2, 50% PEG 200, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.00001 Å
DetectorType: MAR CCD / Detector: CCD / Date: Jul 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 7121 / Num. obs: 7471 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Χ2: 3.039 / Net I/σ(I): 40.189
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.211 / Num. unique all: 748 / Χ2: 1.712 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.88 Å
Translation2.5 Å26.88 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jgo

2jgo


Resolution: 1.86→24.4 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.812 / SU B: 5.843 / SU ML: 0.111 / SU R Cruickshank DPI: 0.178 / SU Rfree: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 344 4.6 %RANDOM
Rwork0.199 ---
obs0.202 7465 98.26 %-
all-7121 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.09 Å2 / Biso mean: 28.08 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.14 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.86→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms708 0 11 70 789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021762
X-RAY DIFFRACTIONr_bond_other_d0.0020.02525
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9841004
X-RAY DIFFRACTIONr_angle_other_deg0.91331296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.825586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39427.81232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58515160
X-RAY DIFFRACTIONr_chiral_restr0.0990.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02110
X-RAY DIFFRACTIONr_nbd_refined0.2790.2225
X-RAY DIFFRACTIONr_nbd_other0.1950.2536
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2344
X-RAY DIFFRACTIONr_nbtor_other0.130.2407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2920.242
X-RAY DIFFRACTIONr_metal_ion_refined0.1930.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.214
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1950.23
X-RAY DIFFRACTIONr_mcbond_it1.2481.5612
X-RAY DIFFRACTIONr_mcbond_other0.3441.5187
X-RAY DIFFRACTIONr_mcangle_it1.4652695
X-RAY DIFFRACTIONr_scbond_it3.2483391
X-RAY DIFFRACTIONr_scangle_it3.8984.5305
LS refinement shellResolution: 1.86→1.905 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 36 -
Rwork0.166 507 -
all-543 -
obs--98.91 %
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)
140.2273-2.5617-28.77738.07461.097421.36640.5588-0.6535-0.084-0.0923-0.170.3052-0.40880.1243-0.3888-0.00230.0027-0.01090.13610.00580.0339-3.2195.341514.1526
254.8569-8.7986-37.64266.52495.555226.85260.2781-0.1890.6483-0.12950.08780.1029-0.3702-0.5867-0.36580.0223-0.00170.0104-0.00130.00870.037910.58913.03913.235
324.72061.73091.062912.486.613424.3944-0.346-0.5664-0.37670.00990.0809-0.12920.42460.65930.26510.03170.02110.0184-0.09260.03510.071420.6319-1.0484-2.1576
474.733719.3165-24.60725.2834-9.291337.65920.3681.65730.0266-0.81350.69790.3066-2.0141-1.6932-1.06590.10450.06670.03920.09080.07810.0125-4.3052-3.559622.1932
531.80059.8751-18.67384.3611-5.204912.80880.2065-0.96320.26070.2003-0.08940.0964-0.2386-0.0617-0.11710.0447-0.06530.00240.07760.04730.06788.0349-0.591417.3435
627.577910.2479-9.765514.8589-1.292818.7122-0.14220.2938-0.3579-0.0893-0.2572-0.39730.09040.00110.39930.0235-0.02830.0011-0.1094-0.00310.034323.94513.66888.2966
755.9195-4.0077-11.93090.28870.83742.756-0.29240.0372-0.48240.0562-0.0016-0.030.2897-0.12460.2940.0518-0.02380.02680.0694-0.01750.0770.181-5.59110.1193
812.7865-14.7281.718220.95326.410618.4907-0.50140.19-0.10220.590.72321.02540.5576-0.1256-0.22180.03260.0130.03-0.09140.00390.110617.755-7.06927.418
941.70079.0377-3.32135.3437-10.082214.81280.3975-0.47180.35850.5518-0.6104-0.0316-0.0120.51540.21280.0066-0.0038-0.0297-0.04360.01150.064125.5615-7.2485.9531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2A13 - 22
3X-RAY DIFFRACTION3A23 - 29
4X-RAY DIFFRACTION4B1 - 5
5X-RAY DIFFRACTION5B6 - 19
6X-RAY DIFFRACTION6B20 - 29
7X-RAY DIFFRACTION7C1 - 19
8X-RAY DIFFRACTION8C20 - 23
9X-RAY DIFFRACTION9C24 - 29

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