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- PDB-6dyk: Iron- and Nitric Oxide-bound structure of the engineered cyt b562... -

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Basic information

Entry
Database: PDB / ID: 6dyk
TitleIron- and Nitric Oxide-bound structure of the engineered cyt b562 variant, CH3Y*
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Designed protein / 4-helix bundle
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
: / NITRIC OXIDE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 Å
AuthorsTezcan, F.A. / Rittle, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120981 United States
National Science Foundation (NSF, United States)CHE1607145 United States
CitationJournal: Nat.Chem. / Year: 2019
Title: An efficient, step-economical strategy for the design of functional metalloproteins.
Authors: Rittle, J. / Field, M.J. / Green, M.T. / Tezcan, F.A.
History
DepositionJul 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562
C: Soluble cytochrome b562
E: Soluble cytochrome b562
G: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8938
Polymers47,7224
Non-polymers1724
Water4,288238
1
A: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,9301
Polymers11,9301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,9301
Polymers11,9301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0163
Polymers11,9301
Non-polymers862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0163
Polymers11,9301
Non-polymers862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.919, 98.690, 178.990
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-255-

HOH

21C-267-

HOH

31E-314-

HOH

41G-319-

HOH

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Components

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


Mass: 11930.375 Da / Num. of mol.: 4
Mutation: M7W, K59W, I67H, G70Y, Q71H, T96C, T97H, Y101A, H102I, R106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABE7
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Drop consists of 2 uL of 25% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 6.0) mixed with 1 uL of 4 mM protein and 2.2 mM Iron(II) Sulfate (Anaerobic crystal growth). ...Details: Drop consists of 2 uL of 25% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 6.0) mixed with 1 uL of 4 mM protein and 2.2 mM Iron(II) Sulfate (Anaerobic crystal growth). Diethylamine NONOate (5 mM) was added to mother liquor prior to crystal harvest

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.73 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73 Å / Relative weight: 1
ReflectionResolution: 1.955→49.345 Å / Num. obs: 31848 / % possible obs: 99.5 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Net I/σ(I): 28.5
Reflection shellResolution: 1.955→2.0039 Å / Redundancy: 12 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 12.2 / Num. unique obs: 3092 / CC1/2: 0.992 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1m6t

1m6t


Resolution: 1.955→49.345 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.99
RfactorNum. reflection% reflection
Rfree0.2486 2000 6.4 %
Rwork0.203 --
obs0.206 31262 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.955→49.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 6 238 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193444
X-RAY DIFFRACTIONf_angle_d0.4054655
X-RAY DIFFRACTIONf_dihedral_angle_d6.8882930
X-RAY DIFFRACTIONf_chiral_restr0.032508
X-RAY DIFFRACTIONf_plane_restr0.003625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.955-2.00390.26321410.23772071X-RAY DIFFRACTION100
2.0039-2.05810.31081440.23742104X-RAY DIFFRACTION99
2.0581-2.11860.28841430.21962081X-RAY DIFFRACTION99
2.1186-2.1870.26851390.20672036X-RAY DIFFRACTION99
2.187-2.26520.25171430.20782110X-RAY DIFFRACTION100
2.2652-2.35590.28851420.20592078X-RAY DIFFRACTION99
2.3559-2.46310.25621430.21572079X-RAY DIFFRACTION98
2.4631-2.5930.27331440.21782107X-RAY DIFFRACTION100
2.593-2.75540.27841450.21852116X-RAY DIFFRACTION100
2.7554-2.96810.22931380.21812034X-RAY DIFFRACTION97
2.9681-3.26680.27271480.21052146X-RAY DIFFRACTION99
3.2668-3.73930.22321420.19482092X-RAY DIFFRACTION98
3.7393-4.71060.22981400.17592055X-RAY DIFFRACTION95
4.7106-49.36070.22161480.192153X-RAY DIFFRACTION94

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