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- PDB-6dy6: Mn(II)-bound structure of the engineered cyt cb562 variant, CH2E -

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Basic information

Entry
Database: PDB / ID: 6dy6
TitleMn(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 transfer activity / periplasmic space / 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: 1.8 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

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)25,2007
Polymers23,6142
Non-polymers1,5855
Water2,324129
1
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5364
Polymers11,8071
Non-polymers7283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6643
Polymers11,8071
Non-polymers8572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.720, 49.000, 117.530
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Drop consists of 1 uL of 30% PEG 400, 200 mM Ammonium Acetate and 0.1 M Tris (pH 8.5) mixed with 1 uL of 2.5 mM protein and 2 mM Manganese(II) Chloride

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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: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.73 Å / Num. obs: 19742 / % possible obs: 99.3 % / Redundancy: 11.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.8487 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1931 / CC1/2: 0.865 / % possible all: 99.6

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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: 1.8→37.634 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.99
RfactorNum. reflection% reflection
Rfree0.2604 1839 9.33 %
Rwork0.2103 --
obs0.2151 19712 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 104 129 1871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011894
X-RAY DIFFRACTIONf_angle_d1.0292558
X-RAY DIFFRACTIONf_dihedral_angle_d9.2111722
X-RAY DIFFRACTIONf_chiral_restr0.043257
X-RAY DIFFRACTIONf_plane_restr0.006334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.40411380.29471339X-RAY DIFFRACTION100
1.8487-1.90310.32981400.28531358X-RAY DIFFRACTION100
1.9031-1.96450.33321400.27151360X-RAY DIFFRACTION99
1.9645-2.03470.31591370.25441337X-RAY DIFFRACTION99
2.0347-2.11620.29781370.24951339X-RAY DIFFRACTION99
2.1162-2.21250.30681400.22841358X-RAY DIFFRACTION99
2.2125-2.32910.32251410.23461365X-RAY DIFFRACTION99
2.3291-2.4750.25941400.23351364X-RAY DIFFRACTION99
2.475-2.6660.29661410.22181369X-RAY DIFFRACTION100
2.666-2.93420.25151430.22691387X-RAY DIFFRACTION100
2.9342-3.35860.26871430.21321394X-RAY DIFFRACTION99
3.3586-4.23060.21281450.17611410X-RAY DIFFRACTION100
4.2306-37.64180.21211540.16821493X-RAY DIFFRACTION99

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