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- PDB-4u9d: Crystal Structure of the Zn-directed tetramer of the engineered c... -

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Basic information

Entry
Database: PDB / ID: 4u9d
TitleCrystal Structure of the Zn-directed tetramer of the engineered cyt cb562 variant, AB3
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / designed enzyme / Zn-coordinating protein / tetramer assembly
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsTezcan, F.A. / Song, W.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1306646 United States
CitationJournal: Science / Year: 2014
Title: A designed supramolecular protein assembly with in vivo enzymatic activity.
Authors: Song, W.J. / Tezcan, F.A.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
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 2.1Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)50,33816
Polymers47,3414
Non-polymers2,99712
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-426 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.830, 54.830, 237.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12B
22C
13C
23D

NCS domain segments:

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

Dom-IDEns-IDRefine codeAuth asym-IDLabel asym-ID
116AA
216BB
126BB
226CC
133CC
233DD

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 11835.262 Da / Num. of mol.: 4 / Fragment: UNP residues 23-128
Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, A89H, T96C, R98C, A100H, Y101C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Plasmid: pET20b(+) / Details (production host): kan+/amp- / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ABE7
#2: Chemical
ChemComp-HEC / HEME C / Heme C


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


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 43.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 400 in 20 mM Tris (pH 8.5) and 0.2 M MgCl2

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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: Jan 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→47.48 Å / Num. obs: 13889

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.5→47.48 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.907 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 679 4.9 %RANDOM
Rwork0.238 13209 --
obs0.2409 13888 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100 Å2 / Biso mean: 70.973 Å2 / Biso min: 25.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å21.18 Å2-0 Å2
2--2.36 Å20 Å2
3----7.67 Å2
Refinement stepCycle: final / Resolution: 2.5→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 180 38 3530
Biso mean--75.81 52.43 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193590
X-RAY DIFFRACTIONr_bond_other_d0.0010.023292
X-RAY DIFFRACTIONr_angle_refined_deg0.9352.0034904
X-RAY DIFFRACTIONr_angle_other_deg0.6953.0027576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0215420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.62326.279172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45915592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.623158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024156
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02820
X-RAY DIFFRACTIONr_mcbond_it1.1157.0141692
X-RAY DIFFRACTIONr_mcbond_other1.1157.0121691
X-RAY DIFFRACTIONr_mcangle_it1.96710.5142108
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1621LOOSE POSITIONAL0.455
1A1621LOOSE THERMAL5.510
2B1621LOOSE POSITIONAL0.475
2B1621LOOSE THERMAL4.9510
3C993LOOSE POSITIONAL0.635
3C628TIGHT THERMAL16.140.5
3C993LOOSE THERMAL15.7110
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 43 -
Rwork0.349 956 -
all-999 -
obs--99.9 %

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