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- PDB-1mhx: Crystal Structures of the redesigned protein G variant NuG1 -

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Basic information

Entry
Database: PDB / ID: 1mhx
TitleCrystal Structures of the redesigned protein G variant NuG1
Componentsimmunoglobulin-binding protein G
KeywordsIMMUNE SYSTEM / alpha-beta protein / redesigned first beta-hairpin
Function / homology
Function and homology information


Protein L, Ig light chain-binding / Protein L b1 domain / Ubiquitin-like (UB roll) - #10 / IgG-binding B / B domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesFinegoldia magna (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNauli, S. / Kuhlman, B. / Le Trong, I. / Stenkamp, R.E. / Teller, D.C. / Baker, D.
CitationJournal: Protein Sci. / 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE SEQUENCE DIFFERS FROM PIR ENTRY A45063 AT RESIDUES 15-25 (PIR RESIDUES 334-344) ...SEQUENCE THE SEQUENCE DIFFERS FROM PIR ENTRY A45063 AT RESIDUES 15-25 (PIR RESIDUES 334-344) 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


Theoretical massNumber of molelcules
Total (without water)7,3591
Polymers7,3591
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.458, 49.458, 103.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-142-

HOH

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Components

#1: Protein immunoglobulin-binding protein G


Mass: 7359.115 Da / Num. of mol.: 1 / Fragment: Redesigned B1 domain / Mutation: T58A
Source method: isolated from a genetically manipulated source
Details: Redesigned first beta-hairpin, variant NuG1 / 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.: 87 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: n-propanol, sodium formate, tris-hcl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris1droppH7.5
28 %n-propanol1reservoir
33.6 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→22.3 Å / Num. obs: 6273 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 92.5
Reflection
*PLUS
Num. obs: 6383 / Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1pga

1pga


Resolution: 1.8→22.3 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.225 267 random
Rwork0.212 --
all0.268 6273 -
obs0.261 5900 -
Refinement stepCycle: LAST / Resolution: 1.8→22.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms504 0 0 87 591
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.006

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