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- PDB-3iq6: Crystal structure of a tetrameric Zn-bound cytochrome cb562 compl... -

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Basic information

Entry
Database: PDB / ID: 3iq6
TitleCrystal structure of a tetrameric Zn-bound cytochrome cb562 complex with covalently and non-covalently stabilized interfaces
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / Tetramer of Four-Helix Bundles with Interfacial Disulfide Bonds / Heme / Iron / Metal-binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsBrodin, J.N. / 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
DepositionAug 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water2,612145
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 area5360 Å2
ΔGint-32 kcal/mol
Surface area19840 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 area5250 Å2
ΔGint-31.5 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.265, 76.770, 177.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain A,B,C,D,E,F,G,H, using restrain)

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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 natural source / Source: (natural) 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.: 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 / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 2000, 0.1M HEPES, 0.15 M Sodium chloride, 1.15 mM Zinc chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: May 16, 2009
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 36885 / Num. obs: 36701 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 4.9
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5295 / Rsym value: 0.356 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HNI

3hni


Resolution: 2.35→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.763 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2550 6.9 %Random
Rwork0.228 ---
all0.238 36701 --
obs0.236 36576 98.6 %-
Solvent computationBsol: 39.728 Å2
Displacement parametersBiso max: 97.37 Å2 / Biso mean: 46.922 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.182 Å20 Å20 Å2
2---10.912 Å20 Å2
3---13.094 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 352 145 7041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.367
X-RAY DIFFRACTIONc_mcbond_it1.8312
X-RAY DIFFRACTIONc_scbond_it3.583
X-RAY DIFFRACTIONc_mcangle_it2.772.5
X-RAY DIFFRACTIONc_scangle_it4.7923.5
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11BX-RAY DIFFRACTION0restrain200
11CX-RAY DIFFRACTION0restrain200
11DX-RAY DIFFRACTION0restrain200
11EX-RAY DIFFRACTION0restrain200
11FX-RAY DIFFRACTION0restrain200
11GX-RAY DIFFRACTION0restrain200
11HX-RAY DIFFRACTION0restrain200
LS refinement shellResolution: 2.35→2.37 Å
RfactorNum. reflection% reflection
Rfree0.397 52 -
Rwork0.306 --
obs-663 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4param19x.hemetoph19x.heme

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