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- PDB-5l31: Crystal structure of an engineered metal-free RIDC1 variant conta... -

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Basic information

Entry
Database: PDB / ID: 5l31
TitleCrystal structure of an engineered metal-free RIDC1 variant containing five disulfide bonds.
Components(Soluble cytochrome b562) x 2
KeywordsELECTRON TRANSPORT / engineered protein / cytochrome / complex
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: 2.4 Å
AuthorsTezcan, F.A. / Churchfield, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1306656 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: De Novo Design of an Allosteric Metalloprotein Assembly with Strained Disulfide Bonds.
Authors: Churchfield, L.A. / Medina-Morales, A. / Brodin, J.D. / Perez, A. / Tezcan, F.A.
History
DepositionAug 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _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 / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.3Nov 6, 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)49,36510
Polymers46,8454
Non-polymers2,5206
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.594, 77.534, 88.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 2 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.300583, -0.952643, 0.046056), (-0.948498, -0.293513, 0.119171), (-0.100009, -0.079505, -0.991805)20.30744, 34.32474, -4.20475
3given(-0.156265, 0.728784, -0.666674), (0.734453, -0.365573, -0.571783), (-0.660425, -0.57899, -0.478131)35.56081, -25.07584, 18.25222
4given(-0.783869, 0.529368, 0.324529), (-0.110949, -0.633653, 0.76562), (0.610934, 0.564139, 0.555434)55.5363, 8.96369, -23.37715

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Components

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


Mass: 11707.218 Da / Num. of mol.: 3 / Fragment: UNP residues 23-128
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: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11723.218 Da / Num. of mol.: 1 / Fragment: UNP residues 23-128
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
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.15 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Drop consists of 1 uL of 45% MPD, and 0.1 M Bis Tris (pH 6.5) mixed with 1.5 uL of 2.8 mM protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2016
RadiationMonochromator: Si (111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→38.77 Å / Num. obs: 17325 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rsym value: 0.067 / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JEA

4jea


Resolution: 2.4→38.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.482 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.643 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26701 866 5 %RANDOM
Rwork0.22501 ---
obs0.22716 16402 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.147 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å20 Å2
2--1.32 Å20 Å2
3----1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.4→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 174 64 3460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193494
X-RAY DIFFRACTIONr_bond_other_d0.0060.023209
X-RAY DIFFRACTIONr_angle_refined_deg1.3022.0134776
X-RAY DIFFRACTIONr_angle_other_deg0.9833.0027383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0415414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.12826.456158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99715570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.03158
X-RAY DIFFRACTIONr_chiral_restr0.0620.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024042
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02782
X-RAY DIFFRACTIONr_mcbond_it1.8095.4951671
X-RAY DIFFRACTIONr_mcbond_other1.8075.4951670
X-RAY DIFFRACTIONr_mcangle_it3.0518.2292080
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A908MEDIUM POSITIONAL0.770.5
2B908MEDIUM POSITIONAL0.740.5
3C908MEDIUM POSITIONAL0.760.5
4D908MEDIUM POSITIONAL0.830.5
1A592TIGHT THERMAL11.680.5
2B592TIGHT THERMAL11.240.5
3C592TIGHT THERMAL12.960.5
4D592TIGHT THERMAL10.630.5
1A908MEDIUM THERMAL11.982
2B908MEDIUM THERMAL11.442
3C908MEDIUM THERMAL13.052
4D908MEDIUM THERMAL10.782
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 62 -
Rwork0.297 1171 -
obs--98.17 %

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