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- PDB-7rwx: Crystal structure of a Zn-bound RIDC1 variant in the presence of ... -

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Basic information

Entry
Database: PDB / ID: 7rwx
TitleCrystal structure of a Zn-bound RIDC1 variant in the presence of reductant
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN
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: 1.6 Å
AuthorsKakkis, A. / Golub, E.
Funding support United States, 3items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 1336-2015 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM112584 United States
National Science Foundation (NSF, United States)CHE-1607145 United States
CitationJournal: Chem.Commun.(Camb.) / Year: 2022
Title: Redox- and metal-directed structural diversification in designed metalloprotein assemblies.
Authors: Kakkis, A. / Golub, E. / Choi, T.S. / Tezcan, F.A.
History
DepositionAug 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,7628
Polymers23,3142
Non-polymers1,4486
Water1,29772
1
A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,52416
Polymers46,6284
Non-polymers2,89612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area11450 Å2
ΔGint-286 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.649, 111.649, 148.326
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-202-

CA

21A-330-

HOH

31A-339-

HOH

41B-322-

HOH

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Components

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


Mass: 11657.113 Da / Num. of mol.: 2
Mutation: R56A, L60A, Q63W, K64S, K81H, D88W, V91I, D95H, D96A, K99H, T118C, R120C, Y123C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HEC / HEME C


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


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.82 Å3/Da / Density % sol: 67.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG400, 0.1 M HEPES, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→80.69 Å / Num. obs: 27879 / % possible obs: 96.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 36.04 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.042 / Rrim(I) all: 0.089 / Net I/σ(I): 8.5
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7175 / CC1/2: 0.898 / Rpim(I) all: 0.185 / Rrim(I) all: 0.366 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 1.6→37.01 Å / SU ML: 0.2339 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.5369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2905 2019 7.24 %
Rwork0.2394 25860 -
obs0.2429 27879 59.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 90 72 1792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01011760
X-RAY DIFFRACTIONf_angle_d1.11842410
X-RAY DIFFRACTIONf_chiral_restr0.0528246
X-RAY DIFFRACTIONf_plane_restr0.0069312
X-RAY DIFFRACTIONf_dihedral_angle_d25.7782628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.29910.588710X-RAY DIFFRACTION0.34
1.64-1.650.771610.574616X-RAY DIFFRACTION3.91
1.72-1.730.458110.71488X-RAY DIFFRACTION1.27
1.89-1.930.56851110.52621410X-RAY DIFFRACTION89.89
1.93-2.020.41282060.41072568X-RAY DIFFRACTION84.44
2.02-2.120.43462450.3993079X-RAY DIFFRACTION99.52
2.12-2.260.4052460.35483066X-RAY DIFFRACTION98.95
2.26-2.430.36072330.31453083X-RAY DIFFRACTION99.22
2.43-2.680.3112370.2713100X-RAY DIFFRACTION99.73
2.68-3.060.28922560.24453110X-RAY DIFFRACTION99.82
3.06-3.860.27082370.22113167X-RAY DIFFRACTION99.94
3.86-37.010.23372450.18043243X-RAY DIFFRACTION99.94

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