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- PDB-3hnk: Crystal structure of the dimeric assembly of the cyt cb562 varian... -

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Basic information

Entry
Database: PDB / ID: 3hnk
TitleCrystal structure of the dimeric assembly of the cyt cb562 variant RIDC-1
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Electron transport
Function / homology
Function and homology information


electron transfer activity / periplasmic space / 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: 2.1 Å
AuthorsSalgado, E.N. / Lewis, R.A. / Brodin, J. / Tezcan, F.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Metal templated design of protein interfaces.
Authors: Salgado, E.N. / Ambroggio, X.I. / Brodin, J.D. / Lewis, R.A. / Kuhlman, B. / Tezcan, F.A.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Oct 13, 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 1.4Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6314
Polymers23,3982
Non-polymers1,2332
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3162
Polymers11,6991
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3162
Polymers11,6991
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.318, 55.484, 72.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 3 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11699.084 Da / Num. of mol.: 2 / Mutation: R34A, L38A, Q41W, K42S, D66W, V69I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 26% PEG 2000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→36.86 Å / Num. all: 12150 / Num. obs: 12085 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1558 / Rsym value: 0.249 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
APEXdata collection
SAINTdata reduction
SADABSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27.75 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.86 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.824 / SU B: 5.404 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 830 6.9 %RANDOM
Rwork0.201 ---
all0.216 12100 --
obs0.205 12023 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 48.74 Å2 / Biso mean: 11.957 Å2 / Biso min: 2.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 86 166 1890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221772
X-RAY DIFFRACTIONr_angle_refined_deg0.9942.0932422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2255210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.03426.58582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36115292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.254154
X-RAY DIFFRACTIONr_chiral_restr0.0730.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021364
X-RAY DIFFRACTIONr_nbd_refined0.2010.2870
X-RAY DIFFRACTIONr_nbtor_refined0.2790.21203
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2158
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.232
X-RAY DIFFRACTIONr_mcbond_it0.3831.51097
X-RAY DIFFRACTIONr_mcangle_it0.67621686
X-RAY DIFFRACTIONr_scbond_it1.2173780
X-RAY DIFFRACTIONr_scangle_it1.9084.5732
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
424TIGHT POSITIONAL0.040.05
395LOOSE POSITIONAL0.575
424TIGHT THERMAL0.070.5
395LOOSE THERMAL0.7910
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 60 -
Rwork0.218 812 -
all-872 -
obs--99.09 %

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