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- PDB-6ai5: Disulfide-free, Zn-directed tetramer of the engineered cyt cb562 ... -

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Basic information

Entry
Database: PDB / ID: 6ai5
TitleDisulfide-free, Zn-directed tetramer of the engineered cyt cb562 variant, C96T/A104AB3
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / de novo protein
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transfer activity / periplasmic space / iron ion binding / heme binding / PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsSong, W.J. / Tezcan, F.A.
Funding support Korea, Republic Of, United States, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1C1B2007898 Korea, Republic Of
National Science Foundation (United States)CHE1306646 United States
CitationJournal: To Be Published
Title: Disulfide-free, Zn-directed tetramer of the engineered cyt cb562 variant, C96T/A104AB3
Authors: Song, W.J. / Tezcan, F.A.
History
DepositionAug 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562
C: Soluble cytochrome b562
E: Soluble cytochrome b562
G: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,36425
Polymers47,1004
Non-polymers3,26421
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, AUC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-475 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.562, 76.871, 96.425
Angle α, β, γ (deg.)90.000, 105.840, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11G-419-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14C
24E
15C
25G
16E
26G

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CB
12AA
22EC
13AA
23GD
14CB
24EC
15CB
25GD
16EC
26GD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ACEG

#1: Protein
Soluble cytochrome b562 / C96T/A104AB3


Mass: 11775.120 Da / Num. of mol.: 4 / Mutation: C96T/A104AB3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7

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Non-polymers , 5 types, 516 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 12.5% PEG 3350, pH 7.5, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9817 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9817 Å / Relative weight: 1
ReflectionResolution: 1.81→38.44 Å / Num. obs: 36906 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.066 / Rsym value: 0.057 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.81-1.910.15653560.9650.0270.0530.045100
5.72-38.440.04512050.9930.0180.0360.03199.6

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→36.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.932 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 1895 5.1 %RANDOM
Rwork0.1753 ---
obs0.1771 34927 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.8 Å2 / Biso mean: 27.084 Å2 / Biso min: 13.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å21.03 Å2
2---1.35 Å2-0 Å2
3---0.65 Å2
Refinement stepCycle: final / Resolution: 1.81→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 189 495 3984
Biso mean--24.66 33.21 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0153596
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173102
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.7394910
X-RAY DIFFRACTIONr_angle_other_deg1.0081.7057243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7845422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56825.525181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47615577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.813158
X-RAY DIFFRACTIONr_chiral_restr0.0660.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024104
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02660
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A32560.1
12C32560.1
21A33070.09
22E33070.09
31A33440.08
32G33440.08
41C31870.11
42E31870.11
51C32280.1
52G32280.1
61E33510.07
62G33510.07
LS refinement shellResolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 132 -
Rwork0.178 2593 -
all-2725 -
obs--100 %

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