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- PDB-3tom: Crystal structure of an engineered cytochrome cb562 that forms 2D... -

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Basic information

Entry
Database: PDB / ID: 3tom
TitleCrystal structure of an engineered cytochrome cb562 that forms 2D, Zn-mediated sheets
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / four helix bundle / electron transfer / periplasmic space
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 / Resolution: 2.3 Å
AuthorsBrodin, J.B. / Tezcan, F.A.
CitationJournal: Nat Chem / Year: 2012
Title: Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays.
Authors: Jeffrey D Brodin / X I Ambroggio / Chunyan Tang / Kristin N Parent / Timothy S Baker / F Akif Tezcan /
Abstract: Proteins represent the most sophisticated building blocks available to an organism and to the laboratory chemist. Yet, in contrast to nearly all other types of molecular building blocks, the designed ...Proteins represent the most sophisticated building blocks available to an organism and to the laboratory chemist. Yet, in contrast to nearly all other types of molecular building blocks, the designed self-assembly of proteins has largely been inaccessible because of the chemical and structural heterogeneity of protein surfaces. To circumvent the challenge of programming extensive non-covalent interactions to control protein self-assembly, we have previously exploited the directionality and strength of metal coordination interactions to guide the formation of closed, homoligomeric protein assemblies. Here, we extend this strategy to the generation of periodic protein arrays. We show that a monomeric protein with properly oriented coordination motifs on its surface can arrange, on metal binding, into one-dimensional nanotubes and two- or three-dimensional crystalline arrays with dimensions that collectively span nearly the entire nano- and micrometre scale. The assembly of these arrays is tuned predictably by external stimuli, such as metal concentration and pH.
History
DepositionSep 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)49,38714
Polymers46,5284
Non-polymers2,85810
Water3,207178
1
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6937
Polymers23,2642
Non-polymers1,4295
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-119 kcal/mol
Surface area11140 Å2
MethodPISA
2
A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6937
Polymers23,2642
Non-polymers1,4295
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-114 kcal/mol
Surface area11070 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-284 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.690, 37.843, 138.489
Angle α, β, γ (deg.)90.000, 112.610, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-130-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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


Mass: 11632.122 Da / Num. of mol.: 4 / Fragment: Soluble cytochrome b562
Mutation: D73H, K77H, R98C, Y101C, K27E, D28K, T31E, R34L, L38A, Q41L, H59R, D66A, V69M, L76A
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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 8 mM ZnCl2 and 200 mM BISTRIS, pH 6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→127.844 Å / Num. all: 19645 / Num. obs: 19645 / % possible obs: 94.3 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rsym value: 0.108 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.423.60.4891.5986927720.48992.8
2.42-2.573.50.3122.3937726430.31292
2.57-2.753.60.2342.9878924700.23492.6
2.75-2.973.50.1614.4816023090.16192.7
2.97-3.253.50.1185.6758021570.11893.8
3.25-3.643.50.0946.9684419780.09495
3.64-4.23.50.1034.7622718040.10396.1
4.2-5.143.60.0579.8568315590.05798.8
5.14-7.273.70.05410.2457712390.05499.8
7.27-47.8023.50.0579.625347140.05799.6

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Phasing

Phasing MRRfactor: 43.29 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.8 Å
Translation2.5 Å47.8 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.8 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.854 / WRfactor Rfree: 0.2908 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7811 / SU B: 21.241 / SU ML: 0.252 / SU R Cruickshank DPI: 0.769 / SU Rfree: 0.3394 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 1283 7.4 %RANDOM
Rwork0.2096 ---
obs0.2153 17350 94.41 %-
all-18379 --
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: 92.77 Å2 / Biso mean: 36.7152 Å2 / Biso min: 15.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.77 Å2
2--0.06 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 178 178 3596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223480
X-RAY DIFFRACTIONr_angle_refined_deg1.3722.1214740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1665420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.31426.75160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.84715616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5641512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212644
X-RAY DIFFRACTIONr_mcbond_it0.3941.52120
X-RAY DIFFRACTIONr_mcangle_it0.72723352
X-RAY DIFFRACTIONr_scbond_it1.37231360
X-RAY DIFFRACTIONr_scangle_it2.2344.51388
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 97 -
Rwork0.181 1149 -
all-1246 -
obs--92.43 %
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)
13.62931.6436-0.43856.2949-0.89212.32220.0161-0.33460.2230.0152-0.03180.27680.11970.36360.01570.05520.05260.00490.1662-0.06390.0805-10.73160.563552.4275
24.37260.2101-4.18030.9764-0.50147.7550.25990.46020.425-0.14850.19230.1740.0805-0.5754-0.45230.08560.0115-0.02360.09790.06770.1993-26.80279.103544.3161
32.15870.84830.37757.501-1.05233.73490.284-0.1582-0.0662-0.1929-0.0375-0.47730.13140.694-0.24640.16030.02520.00720.2767-0.09530.1942.86866.030519.1174
42.51740.3788-3.72741.4083-0.08211.3094-0.11210.36660.2578-0.13050.24460.0290.7977-0.6611-0.13250.254-0.1087-0.07390.17330.03150.1417-14.2439-2.661213.463
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

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