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- PDB-6nl6: Crystal structure of mutant B1 immunoglobulin-binding domain of S... -

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Basic information

Entry
Database: PDB / ID: 6nl6
TitleCrystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q)
ComponentsImmunoglobulin G-binding protein G
KeywordsDE NOVO 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 / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / 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 / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / 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: 1.4 Å
AuthorsHuxford, T. / Stec, B. / Maniaci, B.
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 / Structure summary
Category: audit_author / 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 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_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_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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 1.3Oct 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)25,92714
Polymers25,3924
Non-polymers53410
Water4,756264
1
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4132
Polymers6,3481
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6156
Polymers6,3481
Non-polymers2675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4493
Polymers6,3481
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4493
Polymers6,3481
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.292, 48.292, 83.341
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 6348.063 Da / Num. of mol.: 4
Mutation: T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, D36H, N35K, D36A, N37Q
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): BL21DE3 / References: UniProt: P19909
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 70 mM acetic Acid pH 3.6, 30 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 100 mM NaCl, and 20 mM zinc sulfate
PH range: 3.6 - 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11K, H, -L20.499
ReflectionResolution: 1.4→37.38 Å / Num. obs: 42380 / % possible obs: 95.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.8
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.29 / Num. unique obs: 2092 / % possible all: 70.44

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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: 1.4→37.38 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.131 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.015 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21447 2082 5.1 %RANDOM
Rwork0.14499 ---
obs0.14859 38948 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å2-0 Å2
2---0.41 Å2-0 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.4→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 10 264 2066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0191950
X-RAY DIFFRACTIONr_bond_other_d0.0040.021826
X-RAY DIFFRACTIONr_angle_refined_deg3.1771.9382658
X-RAY DIFFRACTIONr_angle_other_deg1.69934248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7385251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99724.89494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99215352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.928154
X-RAY DIFFRACTIONr_chiral_restr0.1850.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.022198
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02446
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_it3.1861.357928
X-RAY DIFFRACTIONr_mcbond_other3.1871.356927
X-RAY DIFFRACTIONr_mcangle_it3.6292.0471158
X-RAY DIFFRACTIONr_mcangle_other3.6272.0481159
X-RAY DIFFRACTIONr_scbond_it4.7391.7411022
X-RAY DIFFRACTIONr_scbond_other4.7291.7411019
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7982.4691481
X-RAY DIFFRACTIONr_long_range_B_refined5.56513.682581
X-RAY DIFFRACTIONr_long_range_B_other5.42613.2122490
X-RAY DIFFRACTIONr_rigid_bond_restr5.59233776
X-RAY DIFFRACTIONr_sphericity_free25.224587
X-RAY DIFFRACTIONr_sphericity_bonded11.47153905
LS refinement shellResolution: 1.399→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 150 -
Rwork0.172 2092 -
obs--70.44 %

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