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- PDB-1m6t: CRYSTAL STRUCTURE OF B562RIL, A REDESIGNED FOUR HELIX BUNDLE -

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Basic information

Entry
Database: PDB / ID: 1m6t
TitleCRYSTAL STRUCTURE OF B562RIL, A REDESIGNED FOUR HELIX BUNDLE
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / protein design
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsChu, R. / Takei, J. / Knowlton, J.R. / Andrykovitch, M. / Pei, W. / Kajava, A.V. / Steinbach, P.J. / Ji, X. / Bai, Y.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Redesign of a Four-Helix Bundle Protein by Phage Display Coupled with Proteolysis and Structural Characterization by NMR and X-ray Crystallography
Authors: Chu, R. / Takei, J. / Knowlton, J.R. / Andrykovitch, M. / Pei, W. / Kajava, A.V. / Steinbach, P.J. / Ji, X. / Bai, Y.
History
DepositionJul 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / pdbx_initial_refinement_model
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8812
Polymers11,7851
Non-polymers961
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.300, 52.340, 93.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21A-318-

HOH

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Components

#1: Protein Soluble cytochrome b562 / Cytochrome b562


Mass: 11785.229 Da / Num. of mol.: 1 / Mutation: M7W,H102I,R106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cytB562 / Plasmid: Pet-17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P0ABE7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 3.2 M NH4(SO4), 2.44 mM N-octanoylsucrose, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
124 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
32.44 mMN-octanoylsucrose1drop
43.2 Mammonium sulfate1reservoir
50.1 MBicine1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.81→18.9 Å / Num. all: 9252 / Num. obs: 9252 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.3 / Rsym value: 0.03 / Net I/σ(I): 46.1
Reflection shellResolution: 1.81→1.86 Å / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.9 / Num. unique all: 749 / Rsym value: 0.533 / % possible all: 76.8
Reflection
*PLUS
Highest resolution: 1.8 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 76.8 % / Rmerge(I) obs: 0.533

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 256B

256b


Resolution: 1.81→18.9 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 505897.88 / Data cutoff high rms absF: 505897.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 485 5.2 %RANDOM
Rwork0.21 ---
all-9252 --
obs-9252 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.0863 Å2 / ksol: 0.35708 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2---2.31 Å20 Å2
3---1.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-19 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.81→18.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 5 118 950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.772
X-RAY DIFFRACTIONc_scangle_it4.352.5
LS refinement shellResolution: 1.81→1.91 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 69 5.5 %
Rwork0.323 1188 -
obs-1188 79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rfree: 0.344 / Rfactor Rwork: 0.323

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