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- PDB-6nlb: Crystal structure of de novo designed metal-controlled dimer of m... -

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Basic information

Entry
Database: PDB / ID: 6nlb
TitleCrystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-apo
ComponentsImmunoglobulin G-binding protein G
KeywordsMETAL BINDING PROTEIN / Metal-mediated complex / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / struct_conn
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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
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

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
B: Immunoglobulin G-binding protein G
C: Immunoglobulin G-binding protein G
D: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9846
Polymers24,9364
Non-polymers492
Water1,58588
1
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2833
Polymers6,2341
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2341
Polymers6,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2341
Polymers6,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2341
Polymers6,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.892, 42.892, 102.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 6233.942 Da / Num. of mol.: 4 / 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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 31% PEG 4,000 0.1M Tris pH 8.5 200mM MgCl2 / PH range: 7.3-7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.52
11K, H, -L20.48
ReflectionResolution: 2.3→37.15 Å / Num. obs: 7581 / % possible obs: 85.96 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.8
Reflection shellResolution: 2.304→2.363 Å / Num. unique obs: 126 / % possible all: 20.11

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PGA

1pga


Resolution: 2.3→37.15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.882 / SU B: 13.416 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.066 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25762 416 5.2 %RANDOM
Rwork0.18784 ---
obs0.19156 7581 85.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.79 Å2
Baniso -1Baniso -2Baniso -3
1--5.62 Å2-0 Å2-0 Å2
2---5.62 Å2-0 Å2
3---11.25 Å2
Refinement stepCycle: 1 / Resolution: 2.3→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 2 88 1846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191788
X-RAY DIFFRACTIONr_bond_other_d0.0020.021676
X-RAY DIFFRACTIONr_angle_refined_deg2.2461.9262424
X-RAY DIFFRACTIONr_angle_other_deg1.12633868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5865220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.0872680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.41815308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022004
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02388
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_it1.4092.44892
X-RAY DIFFRACTIONr_mcbond_other1.4072.438891
X-RAY DIFFRACTIONr_mcangle_it2.4813.651108
X-RAY DIFFRACTIONr_mcangle_other2.483.6531109
X-RAY DIFFRACTIONr_scbond_it1.1462.479896
X-RAY DIFFRACTIONr_scbond_other1.1462.472893
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9873.6761315
X-RAY DIFFRACTIONr_long_range_B_refined6.03918.7972038
X-RAY DIFFRACTIONr_long_range_B_other5.57718.6852020
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 15 -
Rwork0.18 126 -
obs--20.11 %
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)
12.63011.08-0.55021.0549-0.15240.4554-0.05510.0601-0.06110.0048-0.0302-0.11-0.0455-0.02320.08530.18810.0282-0.02410.20050.00720.0341-21.41326.6826-0.2381
20.03510.0355-0.12721.4336-0.32770.7718-0.03960.020.00680.0644-0.00110.09870.050.09960.04080.1818-0.0045-0.01860.24380.02750.0361-26.579.7003-16.688
33.63941.20710.72374.89130.3890.16-0.09710.17770.6271-0.0957-0.04131.0490.00040.07080.13830.16530.0173-0.01810.1658-0.02890.2806-25.4066-9.881-13.1864
43.3907-0.32780.18652.5918-0.77390.2427-0.3651-0.0324-0.486-0.04340.1426-0.85790.0007-0.08670.22250.1083-0.03360.06340.22620.0150.4078-38.8736-2.2119-4.2275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 56
2X-RAY DIFFRACTION2B1 - 56
3X-RAY DIFFRACTION3C1 - 56
4X-RAY DIFFRACTION4D1 - 56

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