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- PDB-6nla: Crystal structure of de novo designed metal-controlled dimer of B... -

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Basic information

Entry
Database: PDB / ID: 6nla
TitleCrystal structure of de novo designed metal-controlled dimer of B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-zinc
ComponentsImmunoglobulin G-binding protein G
KeywordsDE NOVO PROTEIN / Metal-mediated dimer / B1 Domain of Streptococcal protein G / Immunoglobulin binding protein
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsManiaci, B. / Stec, B. / Huxford, T.
CitationJournal: Biochemistry / Year: 2019
Title: Design of High-Affinity Metal-Controlled Protein Dimers.
Authors: Maniaci, B. / Lipper, C.H. / Anipindi, D.L. / Erlandsen, H. / Cole, J.L. / Stec, B. / Huxford, T. / Love, J.J.
History
DepositionJan 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2019Group: Data collection / Structure summary / Category: audit_author
Revision 1.3May 3, 2023Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6099
Polymers6,2341
Non-polymers3758
Water2,036113
1
A: Immunoglobulin G-binding protein G
hetero molecules

A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,21818
Polymers12,4682
Non-polymers75116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area3380 Å2
ΔGint-233 kcal/mol
Surface area5990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.155, 63.155, 39.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-243-

HOH

21A-254-

HOH

31A-260-

HOH

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Components

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Antibody , 1 types, 1 molecules A

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6233.942 Da / Num. of mol.: 1 / Mutation: L12H, E15V, T16L, T18I, V29H, Y33H, N37L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus (bacteria) / Gene: spg / Plasmid: pET21a / Details (production host): T7 expression / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19909

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Non-polymers , 5 types, 121 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 4M NaCl 0.1M HEPES pH 7.5 50mM MgCl2, 5mM zinc sulfate
PH range: 7.3-7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.0083 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0083 Å / Relative weight: 1
ReflectionResolution: 1.34→31.58 Å / Num. obs: 16453 / % possible obs: 97.95 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.8
Reflection shellResolution: 1.34→1.374 Å / Num. unique obs: 1038 / % possible all: 83.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PGA

1pga


Resolution: 1.34→31.58 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.943 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12786 849 4.9 %RANDOM
Rwork0.10425 ---
obs0.10425 16453 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.219 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.34→31.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms439 0 13 113 565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.013500
X-RAY DIFFRACTIONr_bond_other_d0.0020.017466
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.66686
X-RAY DIFFRACTIONr_angle_other_deg1.5331.5961096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.926569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07826.52223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0171593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0293
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_it2.412.131240
X-RAY DIFFRACTIONr_mcbond_other2.4152.118239
X-RAY DIFFRACTIONr_mcangle_it3.0233.195303
X-RAY DIFFRACTIONr_mcangle_other3.0183.203304
X-RAY DIFFRACTIONr_scbond_it4.8662.559260
X-RAY DIFFRACTIONr_scbond_other4.8572.566261
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9733.657378
X-RAY DIFFRACTIONr_long_range_B_refined6.35530.901620
X-RAY DIFFRACTIONr_long_range_B_other5.64428.697588
X-RAY DIFFRACTIONr_rigid_bond_restr4.9513966
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.339→1.374 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.164 61 -
Rwork0.113 1038 -
obs--83.64 %

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