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- PDB-3h5g: Switching the Chirality of the Metal Environment Alters the Coord... -

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Basic information

Entry
Database: PDB / ID: 3h5g
TitleSwitching the Chirality of the Metal Environment Alters the Coordination Mode in Designed Peptides.
ComponentsCOIL SER L16D-Pen
KeywordsDE NOVO PROTEIN / DE-NOVO PROTEIN / PARALLEL THREE-STRANDED COILED COIL / D-PENICILLAMINE
Function / homologyACETATE ION
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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 L16D-Pen
B: COIL SER L16D-Pen
C: COIL SER L16D-Pen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,57911
Polymers10,0623
Non-polymers5178
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.723, 29.237, 44.385
Angle α, β, γ (deg.)90.00, 119.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-46-

HOH

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Components

#1: Protein/peptide COIL SER L16D-Pen


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


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 30% PEG 200, 5% PEG 3000, pH 6.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MAR CCD / Detector: CCD / Date: Mar 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. all: 8646 / Num. obs: 9096 / % possible obs: 96.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Χ2: 2.205 / Net I/σ(I): 54.026
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.187 / Num. unique all: 387 / Χ2: 0.868 / % possible all: 91.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.86 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.35 Å
Translation2.5 Å33.35 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jgo

2jgo


Resolution: 1.71→14.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.883 / SU B: 2.925 / SU ML: 0.063 / SU R Cruickshank DPI: 0.119 / SU Rfree: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 440 4.8 %RANDOM
Rwork0.181 ---
obs0.183 9085 96.49 %-
all-8646 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.46 Å2 / Biso mean: 29.304 Å2 / Biso min: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.12 Å2
2---0.06 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.71→14.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms708 0 11 57 776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021709
X-RAY DIFFRACTIONr_bond_other_d0.0010.02485
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.983951
X-RAY DIFFRACTIONr_angle_other_deg0.90731193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.058588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10227.30826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02515140
X-RAY DIFFRACTIONr_chiral_restr0.0630.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02112
X-RAY DIFFRACTIONr_nbd_refined0.2450.2199
X-RAY DIFFRACTIONr_nbd_other0.1690.2458
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2343
X-RAY DIFFRACTIONr_nbtor_other0.0910.2357
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.233
X-RAY DIFFRACTIONr_metal_ion_refined0.2630.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1530.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.213
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1120.24
X-RAY DIFFRACTIONr_mcbond_it0.8831.5592
X-RAY DIFFRACTIONr_mcbond_other0.2141.5179
X-RAY DIFFRACTIONr_mcangle_it1.092692
X-RAY DIFFRACTIONr_scbond_it2.2493347
X-RAY DIFFRACTIONr_scangle_it2.9964.5257
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 30 -
Rwork0.168 566 -
all-596 -
obs--91.13 %
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)
128.40368.2995-21.79128.8524-4.802622.17370.7487-0.45090.32760.4325-0.1902-0.0753-0.15780.3946-0.5585-0.0484-0.011-0.04490.07-0.0162-0.0439-4.72874.913915.125
231.7154-7.8186-22.25945.00575.142819.07490.25090.31750.1327-0.0586-0.13550.3015-0.184-0.6072-0.1153-0.0692-0.00190.0049-0.02820.0289-0.01027.96162.69294.4779
324.09650.0502-6.829711.42185.158715.06790.0827-0.2694-0.0239-0.0698-0.0498-0.505-0.13660.4602-0.0329-0.0819-0.00280.0054-0.07850.0429-0.032820.0955-0.8395-2.0178
427.0072.2989-17.622712.1217-6.156451.47930.29511.30520.9601-0.29250.26690.4809-1.1531-0.443-0.562-0.02370.010.01320.0710.0689-0.0548-4.2345-4.120922.1112
554.905316.0136-14.29879.3712-7.287515.60870.5446-0.81820.55180.2569-0.1580.1012-0.4311-0.2858-0.3867-0.028-0.03420.05110.14590.0338-0.06674.6614-1.240818.7098
622.26397.9637-11.33557.402-7.191211.93020.2987-0.2252-0.4530.4859-0.3206-0.1743-0.310.01240.02190.0039-0.0728-0.0144-0.0906-0.0176-0.067220.91252.37829.9103
734.42893.4383-5.087517.22534.879511.3002-0.9395-0.6859-0.14710.56260.2711-0.105-0.3170.0860.6684-0.0353-0.02950.0187-0.0501-0.052-0.0382-9.0589-4.236612.8004
855.9911-3.0046-11.27674.27091.13584.3203-0.17910.107-1.05630.1778-0.14630.35620.2476-0.24540.3255-0.0864-0.04830.0569-0.0604-0.04280.02522.4167-6.85359.1831
927.911-2.3683-1.45927.58670.03537.1361-0.0566-0.3162-0.09760.38790.0516-0.0635-0.11570.0510.005-0.07130.0031-0.0131-0.12-0.0129-0.069620.7782-7.50456.1191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A10 - 21
3X-RAY DIFFRACTION3A22 - 29
4X-RAY DIFFRACTION4B1 - 5
5X-RAY DIFFRACTION5B6 - 14
6X-RAY DIFFRACTION6B15 - 29
7X-RAY DIFFRACTION7C1 - 5
8X-RAY DIFFRACTION8C6 - 17
9X-RAY DIFFRACTION9C18 - 29

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