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- PDB-2zw1: Crystal structure of a Streptococcal protein G B1 mutant -

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Basic information

Entry
Database: PDB / ID: 2zw1
TitleCrystal structure of a Streptococcal protein G B1 mutant
ComponentsProtein LG
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN BINDING DOMAIN / PH-DEPENDENT LIGAND BINDING
Function / homologyProtein L, Ig light chain-binding / Protein L b1 domain / IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / Protein LG
Function and homology information
Biological speciesFinegoldia magna (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWatanabe, H. / Matsumaru, H. / Odahara, T. / Suto, K. / Honda, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Optimizing pH response of affinity between protein G and IgG Fc: how electrostatic modulations affect protein-protein interactions.
Authors: Watanabe, H. / Matsumaru, H. / Ooishi, A. / Feng, Y. / Odahara, T. / Suto, K. / Honda, S.
History
DepositionNov 26, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein LG


Theoretical massNumber of molelcules
Total (without water)6,4371
Polymers6,4371
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.266, 23.266, 178.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein LG / immunoglobulin binding protein


Mass: 6437.115 Da / Num. of mol.: 1 / Fragment: B1 domain / Mutation: Q32H, D36E, N37H, D40H, E42H, D47P, A48E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53291
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.88 Å3/Da / Density % sol: 34.53 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 8862 / Redundancy: 7.8 % / Biso Wilson estimate: 18.111 Å2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→44.68 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.592 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28934 328 4.7 %RANDOM
Rwork0.23469 ---
obs0.23728 6684 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.223 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.84 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 0 65 519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021465
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.92632
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.381556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55725.23821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.511577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02348
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2182
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2310
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3431.5288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.092457
X-RAY DIFFRACTIONr_scbond_it3.0113203
X-RAY DIFFRACTIONr_scangle_it4.5484.5175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 24 -
Rwork0.303 512 -
obs--99.08 %

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