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- PDB-6ds9: Elongated version of a de novo designed three helix bundle struct... -

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Basic information

Entry
Database: PDB / ID: 6ds9
TitleElongated version of a de novo designed three helix bundle structure (GRa3D)
Componentsde novo designed three helix bundle GRa3D
KeywordsDE NOVO PROTEIN / three helix bundle / de novo scaffold
Function / homologyTHIOCYANATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.34 Å
AuthorsKoebke, K.J. / Ruckthong, L.R. / Meagher, J.L. / Stuckey, J.A. / Pecoraro, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES012236 United States
CitationJournal: Inorg Chem / Year: 2018
Title: Clarifying the Copper Coordination Environment in a de Novo Designed Red Copper Protein.
Authors: Koebke, K.J. / Ruckthong, L. / Meagher, J.L. / Mathieu, E. / Harland, J. / Deb, A. / Lehnert, N. / Policar, C. / Tard, C. / Penner-Hahn, J.E. / Stuckey, J.A. / Pecoraro, V.L.
History
DepositionJun 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: de novo designed three helix bundle GRa3D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,75110
Polymers10,2201
Non-polymers5319
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.396, 46.396, 109.303
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-101-

ZN

21A-102-

ZN

31A-104-

SCN

41A-104-

SCN

51A-104-

SCN

61A-231-

HOH

71A-233-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein de novo designed three helix bundle GRa3D


Mass: 10220.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 52 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.22 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M Disodium DL Malate 200 mM Sodium Thiosulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 19532 / % possible obs: 98.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 15.97 Å2 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.016 / Rrim(I) all: 0.037 / Χ2: 0.798 / Net I/σ(I): 16.2 / Num. measured all: 107459
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.34-1.363.60.3248320.9450.1890.3770.85382.1
1.36-1.394.30.3029390.9570.1650.3450.772100
1.39-1.414.80.30510390.9680.1560.3430.789100
1.41-1.445.50.2819460.9810.1320.3110.826100
1.44-1.475.60.19310100.9950.090.2130.819100
1.47-1.515.60.12510120.9980.0580.1380.823100
1.51-1.555.70.129720.9970.0560.1320.868100
1.55-1.595.70.1189790.9940.0550.130.873100
1.59-1.645.70.1079870.9950.050.1180.915100
1.64-1.695.70.0929700.9940.0430.1020.986100
1.69-1.755.70.08510060.9950.0390.0941.016100
1.75-1.825.70.0719750.9960.0330.0781.078100
1.82-1.95.80.0559930.9970.0250.0610.913100
1.9-25.80.0459770.9960.020.0490.73100
2-2.135.80.0349980.9980.0150.0370.593100
2.13-2.295.80.0369840.9980.0160.0390.782100
2.29-2.525.80.0389940.9970.0170.0420.896100
2.52-2.895.80.0339890.9980.0150.0360.821100
2.89-3.645.90.0239860.9990.010.0250.346100
3.64-505.50.029440.9990.010.0230.26294.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.34→9.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.966 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.055 / SU Rfree Blow DPI: 0.052 / SU Rfree Cruickshank DPI: 0.053
RfactorNum. reflection% reflectionSelection details
Rfree0.186 886 4.75 %RANDOM
Rwork0.18 ---
obs0.18 18658 95.5 %-
Displacement parametersBiso max: 154.46 Å2 / Biso mean: 25.51 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.7583 Å20 Å20 Å2
2---0.7583 Å20 Å2
3---1.5165 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: final / Resolution: 1.34→9.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 49 43 812
Biso mean--31.58 32.78 -
Num. residues----93
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d470SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes262HARMONIC5
X-RAY DIFFRACTIONt_it1596HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion102SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1838SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1596HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2880HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion3.01
LS refinement shellResolution: 1.34→1.43 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2234 123 5.27 %
Rwork0.1863 2209 -
all0.1882 2332 -
obs--73.4 %
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)
11.8199-4.0574-1.128.5958-2.64552.03670.05730.3088-0.0651-0.6708-0.05340.46410.0462-0.0583-0.00390.0226-0.0307-0.0665-0.00220.0449-0.084514.0377-9.7243-12.1183
20.95850.44580.29070.8431-0.11072.29250.0445-0.00940.03210.01470.08290.0238-0.0574-0.1643-0.1274-0.00570.00860.0105-0.00970.0102-0.005117.7359-9.30610.1328
30.91231.41070.61171.3249-0.18550.01210.1134-0.015-0.11940.0989-0.054-0.0854-0.2165-0.0727-0.05940.01490.00380.01240.0026-0.0016-0.014819.8284-7.031917.9719
40.5520.06280.94630.1411-0.7873.34820.0305-0.0150.0589-0.00980.10520.0079-0.33160.0327-0.13580.0404-0.00820.0088-0.0320.005-0.030724.3518-2.0621.8448
51.69321.39532.90871.0468-0.11629.5080.01660.10270.10330.15410.22620.2934-0.8899-0.1884-0.24280.08220.07950.0813-0.11660.0302-0.036917.36381.6211.7841
62.68993.3251-3.60112.94281.27860.00170.0937-0.17520.0620.02490.0063-0.27460.0738-0.1874-0.10.0321-0.0468-0.0159-0.0255-0.0393-0.014227.07214.566821.5816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 5}A2 - 5
2X-RAY DIFFRACTION2{A|6 - 18}A6 - 18
3X-RAY DIFFRACTION3{A|19 - 31}A19 - 31
4X-RAY DIFFRACTION4{A|32 - 66}A32 - 66
5X-RAY DIFFRACTION5{A|67 - 87}A67 - 87
6X-RAY DIFFRACTION6{A|88 - 94}A88 - 94

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