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- PDB-6dy4: Fe(II)-bound structure of the engineered cyt cb562 variant, CH2E -

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Basic information

Entry
Database: PDB / ID: 6dy4
TitleFe(II)-bound structure of the engineered cyt cb562 variant, CH2E
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Designed protein / 4-helix bundle / electron transport
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
: / HEME C / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRittle, J. / Tezcan, F.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,9636
Polymers23,6142
Non-polymers1,3494
Water4,053225
1
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4823
Polymers11,8071
Non-polymers6742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4823
Polymers11,8071
Non-polymers6742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.570, 48.370, 116.721
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 / Cytochrome b-562


Mass: 11807.246 Da / Num. of mol.: 2 / Mutation: K59W, I67H, G70Y, Q71H, T96C, T97E, R98C, Y101C
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-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Drop consists of 2 uL of 25% PEG 1500, and 0.1 M Tris (pH 8.5) mixed with 2 uL of 4 mM protein and 2.5 mM Iron(II) Sulfate (Anaerobic crystal growth)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→37.24 Å / Num. obs: 16520 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.9559 Å / Redundancy: 5 % / Rmerge(I) obs: 0.33 / Num. unique obs: 1614 / CC1/2: 0.923 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 1.9→37.24 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.88
RfactorNum. reflection% reflection
Rfree0.2544 1652 10 %
Rwork0.1844 --
obs0.1913 16516 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 88 225 1944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011820
X-RAY DIFFRACTIONf_angle_d0.9282469
X-RAY DIFFRACTIONf_dihedral_angle_d10.6961490
X-RAY DIFFRACTIONf_chiral_restr0.042252
X-RAY DIFFRACTIONf_plane_restr0.005327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95590.33021350.24631209X-RAY DIFFRACTION99
1.9559-2.01910.2961360.22561223X-RAY DIFFRACTION100
2.0191-2.09120.32011360.20541218X-RAY DIFFRACTION100
2.0912-2.17490.25121320.20551192X-RAY DIFFRACTION100
2.1749-2.27390.27521350.20911220X-RAY DIFFRACTION100
2.2739-2.39380.26311380.2081245X-RAY DIFFRACTION100
2.3938-2.54370.29821360.20311233X-RAY DIFFRACTION100
2.5437-2.74010.26981360.20451222X-RAY DIFFRACTION100
2.7401-3.01570.2591380.20461240X-RAY DIFFRACTION100
3.0157-3.45180.24621390.19311246X-RAY DIFFRACTION100
3.4518-4.34790.20411410.14151269X-RAY DIFFRACTION100
4.3479-37.24860.23561500.15421347X-RAY DIFFRACTION100

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