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- PDB-5wll: De Novo Design of Polynuclear Transition Metal Clusters in Helix ... -

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Basic information

Entry
Database: PDB / ID: 5wll
TitleDe Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1
ComponentsHelical Bundle 4DH1
KeywordsDE NOVO PROTEIN / Protein Design / Helical Bundle / Metal Binding
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helical Bundle 4DH1
B: Helical Bundle 4DH1
C: Helical Bundle 4DH1
D: Helical Bundle 4DH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,33411
Polymers12,8234
Non-polymers5117
Water1,33374
1
A: Helical Bundle 4DH1
B: Helical Bundle 4DH1
hetero molecules

A: Helical Bundle 4DH1
B: Helical Bundle 4DH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,58314
Polymers12,8234
Non-polymers76110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7440 Å2
ΔGint-290 kcal/mol
Surface area6450 Å2
MethodPISA
2
C: Helical Bundle 4DH1
D: Helical Bundle 4DH1
hetero molecules

C: Helical Bundle 4DH1
D: Helical Bundle 4DH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0848
Polymers12,8234
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6550 Å2
ΔGint-256 kcal/mol
Surface area6240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.782, 80.782, 64.923
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-209-

HOH

21B-203-

HOH

31C-204-

HOH

41D-201-

HOH

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Components

#1: Protein/peptide
Helical Bundle 4DH1


Mass: 3205.660 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 4.81 Å3/Da / Density % sol: 74.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0% PEG1000, 1.0 M AmSO4 and 0.1 M HEPES pH 7.5

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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
ReflectionResolution: 1.9→70.01 Å / Num. obs: 19614 / % possible obs: 99.2 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 10 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3086 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→70.01 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.953 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23778 809 4.9 %RANDOM
Rwork0.21942 ---
obs0.22035 15869 84.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0.35 Å2-0 Å2
2---0.71 Å20 Å2
3---2.3 Å2
Refinement stepCycle: 1 / Resolution: 1.9→70.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 17 74 999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019958
X-RAY DIFFRACTIONr_bond_other_d0.0020.02961
X-RAY DIFFRACTIONr_angle_refined_deg1.1622.0091290
X-RAY DIFFRACTIONr_angle_other_deg0.89332203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2085106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50523.3959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70715199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7921510
X-RAY DIFFRACTIONr_chiral_restr0.0610.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02185
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_it0.3281.666430
X-RAY DIFFRACTIONr_mcbond_other0.3281.665427
X-RAY DIFFRACTIONr_mcangle_it0.5482.495533
X-RAY DIFFRACTIONr_mcangle_other0.5482.495533
X-RAY DIFFRACTIONr_scbond_it0.361.797528
X-RAY DIFFRACTIONr_scbond_other0.3451.798528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5932.658755
X-RAY DIFFRACTIONr_long_range_B_refined3.08631.0483643
X-RAY DIFFRACTIONr_long_range_B_other3.08531.0423643
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.514 19 -
Rwork0.305 387 -
obs--28.16 %
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)
13.7322-5.15482.00689.7322-3.31562.0258-0.078-0.0828-0.12340.28840.14750.1068-0.04580.0983-0.06940.01550.0101-0.00250.0291-0.0010.006-4.521-4.2558.268
21.7475-2.291-0.61148.74141.14011.641-0.0334-0.01060.0863-0.12920.1148-0.1883-0.009-0.0055-0.08130.00890.00650.00030.0309-0.00330.00693.524-2.1714.649
30.9112-2.0227-0.09437.00340.0640.06240.0605-0.00350.0224-0.21-0.0584-0.1076-0.0116-0.0525-0.00210.10010.03710.00560.08010.00620.0503-17.15635.0294.926
48.5942-8.9347-2.532812.22223.18641.5514-0.1373-0.2660.5059-0.1030.3504-0.6512-0.07170.0984-0.21320.10880.03330.00240.0277-0.01260.0813-12.97535.18112.308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 27
2X-RAY DIFFRACTION2B0 - 27
3X-RAY DIFFRACTION3C0 - 27
4X-RAY DIFFRACTION4D0 - 27

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