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Database: PDB / ID: 5wlm
TitleDe Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH2
ComponentsHelical Bundle 4DH2
KeywordsDE NOVO PROTEIN / Protein Design / Helical Bundle / Metal Binding
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, S.-Q. / Liu, L. / DeGrado, W.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM54616 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles.
Authors: Zhang, S.Q. / Chino, M. / Liu, L. / Tang, Y. / Hu, X. / DeGrado, W.F. / Lombardi, A.
History
DepositionJul 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / Item: _citation.year
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 30, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.matrix[1][2] ..._pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helical Bundle 4DH2
B: Helical Bundle 4DH2
C: Helical Bundle 4DH2
D: Helical Bundle 4DH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3189
Polymers12,9914
Non-polymers3275
Water36020
1
A: Helical Bundle 4DH2
B: Helical Bundle 4DH2
hetero molecules

A: Helical Bundle 4DH2
B: Helical Bundle 4DH2
hetero molecules


  • defined by author&software
  • Evidence: equilibrium centrifugation, A-B chains paired with its closest symmetry-related equivalent A*-B* to form a 4-helix bundle; so do C-D in the same way.
  • 13.4 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)13,38310
Polymers12,9914
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6520 Å2
ΔGint-253 kcal/mol
Surface area6340 Å2
MethodPISA
2
C: Helical Bundle 4DH2
D: Helical Bundle 4DH2
hetero molecules

C: Helical Bundle 4DH2
D: Helical Bundle 4DH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2538
Polymers12,9914
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6780 Å2
ΔGint-252 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.156, 81.156, 66.331
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21B-304-

HOH

31C-303-

HOH

41D-304-

HOH

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Components

#1: Protein/peptide
Helical Bundle 4DH2


Mass: 3247.740 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 4.74 Å3/Da / Density % sol: 74.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.01 M NiCl2, 1.0 M Li2SO4 and 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2015
RadiationMonochromator: Double-Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.674
11-h,-k,l20.326
ReflectionResolution: 1.95→48.24 Å / Num. obs: 17954 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2867 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EH1

4eh1


Resolution: 1.95→48.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.695 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18747 474 4.6 %RANDOM
Rwork0.17159 ---
obs0.17228 17954 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.046 Å2
Baniso -1Baniso -2Baniso -3
1--10.65 Å2-0 Å2-0 Å2
2---10.65 Å2-0 Å2
3---21.31 Å2
Refinement stepCycle: 1 / Resolution: 1.95→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 9 20 945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019928
X-RAY DIFFRACTIONr_bond_other_d0.0040.02940
X-RAY DIFFRACTIONr_angle_refined_deg1.1172.0061248
X-RAY DIFFRACTIONr_angle_other_deg0.9332156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7265100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41823.92956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99615200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.622158
X-RAY DIFFRACTIONr_chiral_restr0.0670.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02168
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1911.59424
X-RAY DIFFRACTIONr_mcbond_other0.1911.59422
X-RAY DIFFRACTIONr_mcangle_it0.2542.383524
X-RAY DIFFRACTIONr_mcangle_other0.2542.383524
X-RAY DIFFRACTIONr_scbond_it0.1651.611504
X-RAY DIFFRACTIONr_scbond_other0.1651.611505
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2512.412725
X-RAY DIFFRACTIONr_long_range_B_refined1.3929.4333561
X-RAY DIFFRACTIONr_long_range_B_other1.38829.3723558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.946→1.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 67 -
Rwork0.238 1260 -
obs--97.5 %
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)
17.13836.51561.209812.30232.63513.275-0.0174-0.1792-0.15320.1027-0.04490.0840.108-0.12140.06230.21220.0262-0.00040.14710.03290.01741.5271-4.6897-5.4902
28.9228.0381-1.545414.275-2.51952.6911-0.02050.01210.0937-0.07620.02340.11050.0237-0.0686-0.00290.16740.0048-0.01620.1456-0.02260.006-4.4661.6246-4.2965
38.15127.8748-2.32229.7089-1.57471.6356-0.1010.20690.65050.02710.38790.7494-0.08860.0202-0.28690.4311-0.1067-0.01710.28270.03270.3585-26.7275-35.279-3.7256
42.68684.41970.048313.719-0.53061.19180.05350.03750.2910.34880.10120.67530.071-0.0569-0.15470.3817-0.12750.06280.2688-0.01620.3196-24.563-33.61784.6687
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 26
2X-RAY DIFFRACTION2B0 - 26
3X-RAY DIFFRACTION3C0 - 26
4X-RAY DIFFRACTION4D0 - 26

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