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- PDB-3m79: A tetrameric Zn-bound cytochrome cb562 complex with covalently an... -

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Basic information

Entry
Database: PDB / ID: 3m79
TitleA tetrameric Zn-bound cytochrome cb562 complex with covalently and non-covalently stabilized interfaces crystallized in the presence of Cu(II) and Zn(II)
ComponentsSoluble cytochrome b562
KeywordsOXIDOREDUCTASE / Tetramer of Four Helix Bundles / Electron transport / Heme / Iron / Metal-binding / Transport
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / 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
PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrodin, J.D. / Tezcan, F.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Evolution of metal selectivity in templated protein interfaces.
Authors: Brodin, J.D. / Medina-Morales, A. / Ni, T. / Salgado, E.N. / Ambroggio, X.I. / Tezcan, F.A.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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.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.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 1.3Sep 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
Revision 1.4Oct 30, 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
E: Soluble cytochrome b562
F: Soluble cytochrome b562
G: Soluble cytochrome b562
H: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,06424
Polymers93,6098
Non-polymers5,45516
Water7,116395
1
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)49,53212
Polymers46,8044
Non-polymers2,7288
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-270 kcal/mol
Surface area18730 Å2
MethodPISA
2
E: Soluble cytochrome b562
F: Soluble cytochrome b562
G: Soluble cytochrome b562
H: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,53212
Polymers46,8044
Non-polymers2,7288
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-273 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.547, 78.068, 178.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

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
3CC
4DD
5EE
6FF
7GG
8HH
DetailsTetramer

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Components

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


Mass: 11701.123 Da / Num. of mol.: 8
Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, K77H, T96C, R98C, Y101C
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


Mass: 616.487 Da / Num. of mol.: 8 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.36 Å3/Da / Density % sol: 47.94 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2010
Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing)
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.099→89.17 Å / Num. all: 49272 / Num. obs: 49272 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rsym value: 0.102 / Net I/σ(I): 4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 6358 / Rsym value: 0.176 / % possible all: 84.2

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IQ6

3iq6


Resolution: 2.1→59.87 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.891 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU B: 9.153 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.325 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3566 7.2 %RANDOM
Rwork0.222 ---
all0.23 52736 --
obs0.225 49203 93.3 %-
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: 92.21 Å2 / Biso mean: 27.461 Å2 / Biso min: 9.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→59.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 352 395 7291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227096
X-RAY DIFFRACTIONr_angle_refined_deg1.0952.0939680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0685840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.28726.585328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.866151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0431516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025456
X-RAY DIFFRACTIONr_nbd_refined0.2020.23567
X-RAY DIFFRACTIONr_nbtor_refined0.2780.24820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2379
X-RAY DIFFRACTIONr_metal_ion_refined0.090.225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.220
X-RAY DIFFRACTIONr_mcbond_it0.441.54382
X-RAY DIFFRACTIONr_mcangle_it0.79826736
X-RAY DIFFRACTIONr_scbond_it1.47533122
X-RAY DIFFRACTIONr_scangle_it2.1514.52928
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A420TIGHT POSITIONAL0.040.05
B420TIGHT POSITIONAL0.040.05
C420TIGHT POSITIONAL0.040.05
D420TIGHT POSITIONAL0.030.05
E420TIGHT POSITIONAL0.050.05
F420TIGHT POSITIONAL0.030.05
G420TIGHT POSITIONAL0.030.05
H420TIGHT POSITIONAL0.040.05
A384LOOSE POSITIONAL0.565
B384LOOSE POSITIONAL0.565
C384LOOSE POSITIONAL0.665
D384LOOSE POSITIONAL0.575
E384LOOSE POSITIONAL1.015
F384LOOSE POSITIONAL0.565
G384LOOSE POSITIONAL0.595
H384LOOSE POSITIONAL0.825
A420TIGHT THERMAL0.080.5
B420TIGHT THERMAL0.070.5
C420TIGHT THERMAL0.060.5
D420TIGHT THERMAL0.070.5
E420TIGHT THERMAL0.080.5
F420TIGHT THERMAL0.070.5
G420TIGHT THERMAL0.070.5
H420TIGHT THERMAL0.070.5
A384LOOSE THERMAL1.2
B384LOOSE THERMAL1.01
C384LOOSE THERMAL1.34
D384LOOSE THERMAL1.36
E384LOOSE THERMAL1.69
F384LOOSE THERMAL1.21
G384LOOSE THERMAL1.12
H384LOOSE THERMAL1.32
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 238 -
Rwork0.218 2963 -
all-3201 -
obs--83.6 %
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)
10.7972-0.02630.00311.8990.73182.87720.04580.0315-0.0457-0.09180.01180.0711-0.1312-0.0175-0.0576-0.1184-0.0209-0.002-0.07910.0052-0.095534.7927-6.808465.3531
21.53030.74950.17812.3049-2.19683.613-0.0399-0.0120.2055-0.01470.11640.0747-0.0451-0.3145-0.0764-0.0920.01780.0048-0.0338-0.0137-0.061418.18336.822472.3045
33.6479-2.79871.39655.8287-2.31932.86020.0195-0.390.6440.27810.0668-0.2465-0.7617-0.1139-0.08620.23980.00720.0888-0.0156-0.08960.052832.681420.776975.924
44.5222-0.05321.24671.464-0.97482.03440.00130.11230.0913-0.06110.0128-0.1515-0.1390.0545-0.0141-0.0635-0.03390.0677-0.0958-0.0155-0.040346.0269.548861.5805
50.4101-0.3453-0.28932.11491.04474.59280.0112-0.0146-0.0215-0.09930.0330.0115-0.04160.0665-0.0441-0.10680.0221-0.0097-0.07080.0008-0.135.3976-25.3259109.4367
62.03281.0065-0.80942.6046-2.24713.1802-0.02150.11410.1851-0.16090.03250.26250.1093-0.224-0.011-0.09910.043-0.038-0.0425-0.0506-0.022418.3661-11.9013116.0319
71.4291-1.00991.58372.9739-1.72983.13710.0127-0.05640.1679-0.0772-0.06880.004-0.33240.10190.0561-0.01210.0153-0.0244-0.0622-0.038-0.076432.47511.7227121.3974
85.1769-1.23333.55360.994-1.26553.6424-0.18580.5793-0.1019-0.03710.0593-0.0979-0.26590.54440.1266-0.0484-0.00810.00910.0487-0.0227-0.075446.8449-8.4635107.3964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 106
2X-RAY DIFFRACTION2B1 - 106
3X-RAY DIFFRACTION3C1 - 106
4X-RAY DIFFRACTION4D1 - 106
5X-RAY DIFFRACTION5E1 - 106
6X-RAY DIFFRACTION6F1 - 106
7X-RAY DIFFRACTION7G1 - 106
8X-RAY DIFFRACTION8H1 - 106

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