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- PDB-3iq5: Crystal structure of an engineered metal-free tetrameric cytochro... -

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Basic information

Entry
Database: PDB / ID: 3iq5
TitleCrystal structure of an engineered metal-free tetrameric cytochrome cb562 complex templated by Zn-coordination
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 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 / molecular replacement / Resolution: 2.05 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 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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_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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2708
Polymers46,8044
Non-polymers2,4664
Water4,252236
1
A: Soluble cytochrome b562
C: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
C: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2708
Polymers46,8044
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area8600 Å2
ΔGint-106 kcal/mol
Surface area19920 Å2
MethodPISA
2
B: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules

B: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2708
Polymers46,8044
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area8620 Å2
ΔGint-99 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.153, 69.153, 186.935
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11D-208-

HOH

Noncrystallographic symmetry (NCS)NCS domain: (Details: chain A,B,C,D, using restrain)
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO DIMERIC HALVES (CHAINS A/C, AND CHAINS B/D) OF TWO TETRAMERS. THE GENERATING OF FULL TETRAMERS IS DESCRIBED IN REMARK 350

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Components

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


Mass: 11701.123 Da / Num. of mol.: 4
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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 400, 0.1M Bis-Tris, 0.15M Sodium chloride, pH 6.5, 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: Jan 30, 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: 2.05→50 Å / Num. all: 27396 / Num. obs: 27287 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4021 / Rsym value: 0.448 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HNI

3hni


Resolution: 2.05→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.767 / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1885 6.9 %Random
Rwork0.229 ---
all0.238 27287 --
obs0.229 27222 99.3 %-
Solvent computationBsol: 56.116 Å2
Displacement parametersBiso max: 89.34 Å2 / Biso mean: 37.552 Å2 / Biso min: 11.33 Å2
Baniso -1Baniso -2Baniso -3
1-3.139 Å20 Å20 Å2
2--3.139 Å20 Å2
3----6.279 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 172 236 3680
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.457
X-RAY DIFFRACTIONc_mcbond_it1.7652
X-RAY DIFFRACTIONc_scbond_it3.3553
X-RAY DIFFRACTIONc_mcangle_it2.4192.5
X-RAY DIFFRACTIONc_scangle_it4.3233.5
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11BX-RAY DIFFRACTION0restrain200
11CX-RAY DIFFRACTION0restrain200
11DX-RAY DIFFRACTION0restrain200
LS refinement shellResolution: 2.05→2.07 Å
RfactorNum. reflection% reflection
Rfree0.353 42 -
Rwork0.323 --
obs-696 100 %
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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