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- PDB-1lm3: A Multi-generation Analysis of Cytochrome b562 Redox Variants: Ev... -

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Basic information

Entry
Database: PDB / ID: 1lm3
TitleA Multi-generation Analysis of Cytochrome b562 Redox Variants: Evolutionary Strategies for Modulating Redox Potential Revealed Using a Library Approach
ComponentsSOLUBLE CYTOCHROME B562
KeywordsELECTRON TRANSPORT / four helix bundle / cytochrome / heme-binding
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
PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSprings, S.L. / Bass, S.E. / Bowman, G. / Nodelman, I. / Schutt, C.E. / McLendon, G.L.
CitationJournal: Biochemistry / Year: 2002
Title: A multigeneration analysis of cytochrome b(562) redox variants: evolutionary strategies for modulating redox potential revealed using a library approach.
Authors: Springs, S.L. / Bass, S.E. / Bowman, G. / Nodelman, I. / Schutt, C.E. / McLendon, G.L.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 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
B: SOLUBLE CYTOCHROME B562
D: SOLUBLE CYTOCHROME B562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7807
Polymers23,4742
Non-polymers1,3065
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.098, 48.995, 114.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SOLUBLE CYTOCHROME B562


Mass: 11737.188 Da / Num. of mol.: 2 / Mutation: F61I, F65Y, R106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cycB / Plasmid: pRW1 / Production host: Escherichia coli (E. coli) / Strain (production host): MV1190 / References: UniProt: P0ABE7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 302 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% polyethylene glycol 4000, 0.1M MgCl2, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 302K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 26, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 6896 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 8.2 / Num. unique all: 672 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 49249 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.287

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.333 714 random
Rwork0.232 --
all-6923 -
obs-6462 -
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 89 64 1795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor obs: 0.232 / Rfactor Rfree: 0.333 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS

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