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- PDB-3hnl: Crystal structure of the Cu-induced dimer of the engineered cyt c... -

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Basic information

Entry
Database: PDB / ID: 3hnl
TitleCrystal structure of the Cu-induced dimer of the engineered cyt cb562 variant RIDC-1
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Electron transport
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
COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSalgado, E.N. / Lewis, R.A. / Brodin, J. / Tezcan, F.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Metal templated design of protein interfaces.
Authors: Salgado, E.N. / Ambroggio, X.I. / Brodin, J.D. / Lewis, R.A. / Kuhlman, B. / Tezcan, F.A.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
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.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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8298
Polymers23,3982
Non-polymers1,4316
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-80 kcal/mol
Surface area10920 Å2
MethodPISA
2
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)49,65816
Polymers46,7964
Non-polymers2,86212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10090 Å2
ΔGint-167 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.165, 87.045, 80.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-167-

HOH

21B-128-

HOH

31B-206-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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: 3 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 11699.084 Da / Num. of mol.: 2 / Mutation: R34A, L38A, Q41W, K42S, D66W, V69I
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, 200 mM sodium chloride, 25% PEG 3350, 10.7 mM copper sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Aug 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→22.2 Å / Num. all: 12174 / Num. obs: 12016 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.12 % / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / Num. unique all: 1473 / Rsym value: 0.48 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
APEXdata collection
SAINTdata reduction
SADABSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QLA

2qla


Resolution: 2.2→22.2 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.783 / SU B: 11.375 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.346 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 832 6.9 %RANDOM
Rwork0.204 ---
all0.208 12174 --
obs0.208 11999 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 44.91 Å2 / Biso mean: 13.357 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 90 207 1935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221772
X-RAY DIFFRACTIONr_angle_refined_deg1.1042.0932422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6445210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.33726.58582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14615292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.924154
X-RAY DIFFRACTIONr_chiral_restr0.0750.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021364
X-RAY DIFFRACTIONr_nbd_refined0.2060.2956
X-RAY DIFFRACTIONr_nbtor_refined0.2820.21199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2155
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.237
X-RAY DIFFRACTIONr_mcbond_it0.3731.51089
X-RAY DIFFRACTIONr_mcangle_it0.67621686
X-RAY DIFFRACTIONr_scbond_it1.1783779
X-RAY DIFFRACTIONr_scangle_it1.874.5732
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
424TIGHT POSITIONAL0.050.05
395LOOSE POSITIONAL0.485
424TIGHT THERMAL0.060.5
395LOOSE THERMAL0.9110
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 66 -
Rwork0.233 779 -
all-845 -
obs--96.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54430.2899-0.73021.62450.36483.3576-0.032-0.0234-0.07360.01630.0209-0.11520.12040.18090.011-0.05220.0204-0.0242-0.12680.0029-0.021712.341-11.18721.578
21.38880.01980.72461.53990.18493.1556-0.0815-0.02630.0361-0.01250.021-0.0665-0.24750.1390.0605-0.0355-0.02170.0155-0.1199-0.00910.014211.9698.21418.761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 106
2X-RAY DIFFRACTION2B1 - 106

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