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- PDB-6dy8: Mn(II)-bound structure of the engineered cyt cb562 variant, CH2EY -

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Basic information

Entry
Database: PDB / ID: 6dy8
TitleMn(II)-bound structure of the engineered cyt cb562 variant, CH2EY
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
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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Nov 13, 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
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,23710
Polymers47,6534
Non-polymers2,5846
Water3,135174
1
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5322
Polymers11,9131
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5873
Polymers11,9131
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5873
Polymers11,9131
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5322
Polymers11,9131
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.661, 37.591, 77.323
Angle α, β, γ (deg.)90.00, 104.39, 90.00
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 11913.368 Da / Num. of mol.: 4 / 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-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Drop consists of 1 uL of 25% PEG 1500, 200 mM Calcium Chloride, and 0.1 M Tris (pH 8.5) mixed with 1 uL of 3.5 mM protein and 3.5 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: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→37.59 Å / Num. obs: 33090 / % possible obs: 98 % / Redundancy: 2.7 % / CC1/2: 0.978 / Rmerge(I) obs: 0.134 / Net I/σ(I): 3.2
Reflection shellResolution: 1.9→1.9514 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1 / Num. unique obs: 3296 / CC1/2: 0.832 / % possible all: 98.7

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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→37.59 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.76
RfactorNum. reflection% reflection
Rfree0.2784 1795 5.42 %
Rwork0.2258 --
obs0.2286 33088 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 174 174 3646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013623
X-RAY DIFFRACTIONf_angle_d0.6544920
X-RAY DIFFRACTIONf_dihedral_angle_d21.3272176
X-RAY DIFFRACTIONf_chiral_restr0.032497
X-RAY DIFFRACTIONf_plane_restr0.003649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.34271420.28562398X-RAY DIFFRACTION99
1.9514-2.00880.34621300.28952401X-RAY DIFFRACTION99
2.0088-2.07360.3231400.26772379X-RAY DIFFRACTION98
2.0736-2.14780.30461390.25712376X-RAY DIFFRACTION97
2.1478-2.23370.28531330.24042327X-RAY DIFFRACTION95
2.2337-2.33540.2941350.23922417X-RAY DIFFRACTION99
2.3354-2.45850.31271330.24052401X-RAY DIFFRACTION99
2.4585-2.61250.2881360.24312397X-RAY DIFFRACTION98
2.6125-2.81410.29081360.24952379X-RAY DIFFRACTION97
2.8141-3.09720.31511350.24352443X-RAY DIFFRACTION99
3.0972-3.54510.28981460.22822396X-RAY DIFFRACTION97
3.5451-4.46530.23291430.18962466X-RAY DIFFRACTION99
4.4653-37.59830.24771470.19812513X-RAY DIFFRACTION98

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