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- PDB-6dyf: Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y -

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Basic information

Entry
Database: PDB / ID: 6dyf
TitleCu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Designed protein / 4-helix bundle / electron transport
Function / homology
Function and homology information


electron transport chain / electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
COPPER (II) ION / HEME C / DI(HYDROXYETHYL)ETHER / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.4Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2877
Polymers23,8452
Non-polymers1,4425
Water6,666370
1
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6043
Polymers11,9221
Non-polymers6822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6824
Polymers11,9221
Non-polymers7603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.742, 82.882, 38.528
Angle α, β, γ (deg.)90.00, 98.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 11922.401 Da / Num. of mol.: 2 / Mutation: K59W, I67H, G70Y, Q71H, T96C, T97H, 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

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Non-polymers , 5 types, 375 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Drop consists of 2 uL of 30% PEG 400, 200 mM Magnesium Choride and 0.1 M Bis-Tris (pH 5.5) mixed with 1 uL of 2.7 mM protein and 1.5 mM Copper(II) Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 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 Å / Relative weight: 1
ReflectionResolution: 1.1→41.441 Å / Num. obs: 87061 / % possible obs: 87.05 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.8
Reflection shellResolution: 1.1→1.1297 Å / Redundancy: 6 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 7327 / CC1/2: 0.941 / % possible all: 84.45

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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: 2bc5

2bc5


Resolution: 1.1→41.441 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.05
RfactorNum. reflection% reflection
Rfree0.1649 1769 2.09 %
Rwork0.1469 --
obs0.1473 84506 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→41.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 95 370 2121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091949
X-RAY DIFFRACTIONf_angle_d1.0442670
X-RAY DIFFRACTIONf_dihedral_angle_d23.814738
X-RAY DIFFRACTIONf_chiral_restr0.22263
X-RAY DIFFRACTIONf_plane_restr0.006358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.12970.19291180.20165476X-RAY DIFFRACTION84
1.1297-1.1630.20471240.17865813X-RAY DIFFRACTION89
1.163-1.20050.20491300.16646092X-RAY DIFFRACTION93
1.2005-1.24340.19671380.16816423X-RAY DIFFRACTION98
1.2434-1.29320.20551390.15426517X-RAY DIFFRACTION100
1.2932-1.35210.15421390.14626508X-RAY DIFFRACTION100
1.3521-1.42340.1711400.13516580X-RAY DIFFRACTION100
1.4234-1.51260.14411400.12976548X-RAY DIFFRACTION100
1.5126-1.62940.15531390.12876508X-RAY DIFFRACTION100
1.6294-1.79330.16091420.14216571X-RAY DIFFRACTION100
1.7933-2.05280.1811390.15036545X-RAY DIFFRACTION100
2.0528-2.58630.15271390.14296532X-RAY DIFFRACTION99
2.5863-41.47040.15931420.14766624X-RAY DIFFRACTION100

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