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- PDB-1mi0: Crystal Structure of the redesigned protein G variant NuG2 -

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Basic information

Entry
Database: PDB / ID: 1mi0
TitleCrystal Structure of the redesigned protein G variant NuG2
Componentsimmunoglobulin-binding protein G
KeywordsIMMUNE SYSTEM / alpha-beta protein / redesigned beta-hairpin
Function / homology
Function and homology information


Protein 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
Similarity search - Domain/homology
Biological speciesFinegoldia magna (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNauli, S. / Kuhlman, B. / Le Trong, I. / Stenkamp, R.E. / Teller, D.C. / Baker, D.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2
Authors: Nauli, S. / Kuhlman, B. / Le Trong, I. / Stenkamp, R.E. / Teller, D.C. / Baker, D.
History
DepositionAug 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED
Remark 999SEQUENCE THE SEQUENCE DIFFERS FROM PIR ENTRY A45063 AT RESIDUES 11-21, chain A, and residues 12-22, ...SEQUENCE THE SEQUENCE DIFFERS FROM PIR ENTRY A45063 AT RESIDUES 11-21, chain A, and residues 12-22, chain B, (PIR RESIDUES 328-384) BECAUSE THE AUTHORS REDESIGNED THE FIRST HAIRPIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: immunoglobulin-binding protein G
B: immunoglobulin-binding protein G


Theoretical massNumber of molelcules
Total (without water)14,7122
Polymers14,7122
Non-polymers00
Water1,982110
1
A: immunoglobulin-binding protein G


Theoretical massNumber of molelcules
Total (without water)7,3561
Polymers7,3561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: immunoglobulin-binding protein G


Theoretical massNumber of molelcules
Total (without water)7,3561
Polymers7,3561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.330, 73.790, 39.180
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-108-

HOH

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Components

#1: Protein immunoglobulin-binding protein G


Mass: 7356.045 Da / Num. of mol.: 2 / Fragment: Redesigned B1 domain / Mutation: D52A
Source method: isolated from a genetically manipulated source
Details: REDESIGNED FIRST BETA-HAIRPIN, VARIANT NUG2 / Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Production host: Escherichia coli (E. coli) / References: PIR: A45063, UniProt: Q53291*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, tris-hcl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMHEPES1droppH7.5
21.6 Mammonium sulfate1reservoir
30.1 MTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→19.84 Å / Num. all: 11456 / Num. obs: 11456
Reflection shellResolution: 1.85→1.93 Å / % possible all: 83
Reflection
*PLUS
Num. obs: 10905 / % possible obs: 97.3 % / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.84 Å
RfactorNum. reflection
Rfree0.265 1148
Rwork0.26 -
all0.293 11119
obs0.291 11119
Refinement stepCycle: LAST / Resolution: 1.85→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 0 110 1052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg3.8
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 9780 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS

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