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- PDB-7rww: Crystal structure of a Zn-bound RIDC1 variant -

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Basic information

Entry
Database: PDB / ID: 7rww
TitleCrystal structure of a Zn-bound RIDC1 variant
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: 1.7 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 1.3Nov 13, 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
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,14118
Polymers46,6284
Non-polymers3,51214
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Assembly was characterized in solution using sedimentation velocity analytical ultracentrifugation.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-305 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.791, 86.913, 49.176
Angle α, β, γ (deg.)90.000, 109.163, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 11657.113 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 265 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 45% MPD, 0.1 M HEPES, 0.2 M MgCl2

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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: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→80.85 Å / Num. obs: 40172 / % possible obs: 99.9 % / Redundancy: 14.8 % / Biso Wilson estimate: 22.14 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.032 / Rrim(I) all: 0.126 / Net I/σ(I): 11.7
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3987 / CC1/2: 0.617 / Rpim(I) all: 0.341 / Rrim(I) all: 0.849

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Processing

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

2bc5


Resolution: 1.7→35.96 Å / SU ML: 0.1775 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 2080 5.18 %
Rwork0.1748 38092 -
obs0.1765 40172 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.86 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 224 251 3735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01183732
X-RAY DIFFRACTIONf_angle_d1.12375136
X-RAY DIFFRACTIONf_chiral_restr0.0481516
X-RAY DIFFRACTIONf_plane_restr0.0067670
X-RAY DIFFRACTIONf_dihedral_angle_d23.33881346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.25071370.21172503X-RAY DIFFRACTION96.53
1.74-1.780.23771480.20822543X-RAY DIFFRACTION96.42
1.78-1.830.28781500.21152503X-RAY DIFFRACTION95.91
1.83-1.890.23861350.20832554X-RAY DIFFRACTION96.04
1.89-1.950.23981410.19922397X-RAY DIFFRACTION92.7
1.95-2.020.22651250.19242564X-RAY DIFFRACTION96.97
2.02-2.10.25861410.18522555X-RAY DIFFRACTION97.22
2.1-2.190.20671150.17782590X-RAY DIFFRACTION96.92
2.19-2.310.20591510.17532506X-RAY DIFFRACTION95.99
2.31-2.450.21221340.17552511X-RAY DIFFRACTION95.04
2.45-2.640.18511320.16842573X-RAY DIFFRACTION97.51
2.64-2.910.22821560.16482550X-RAY DIFFRACTION97.41
2.91-3.330.18841350.17122556X-RAY DIFFRACTION96.21
3.33-4.190.16131380.14492577X-RAY DIFFRACTION97.07
4.19-35.960.21671420.18332610X-RAY DIFFRACTION96.9

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