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- PDB-3m4c: A Zn-mediated tetrahedral protein lattice cage encapsulating a mi... -

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Basic information

Entry
Database: PDB / ID: 3m4c
TitleA Zn-mediated tetrahedral protein lattice cage encapsulating a microperoxidase
Components
  • Heme-Peptide Fragment
  • Soluble cytochrome b562
KeywordsELECTRON TRANSPORT / Four-helix bundle / Heme / 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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTezcan, F.A. / Ni, T.W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Structural characterization of a microperoxidase inside a metal-directed protein cage.
Authors: Ni, T.W. / Tezcan, F.A.
History
DepositionMar 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / 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_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_assembly_prop.biol_id / _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.pdbx_leaving_atom_flag / _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

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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: Heme-Peptide Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,56024
Polymers47,5875
Non-polymers3,97319
Water7,909439
1
A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
E: Heme-Peptide Fragment
hetero molecules

A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
E: Heme-Peptide Fragment
hetero molecules

A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
E: Heme-Peptide Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,68072
Polymers142,76215
Non-polymers11,91857
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area41860 Å2
ΔGint-1565 kcal/mol
Surface area54980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.892, 126.892, 167.944
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11D-284-

HOH

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

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 106
2115B1 - 106
3115C1 - 106
4115D1 - 106

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ABCDE

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


Mass: 11645.060 Da / Num. of mol.: 4
Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, I67C, V69I, D73H, D74A, K77H, 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: Protein/peptide Heme-Peptide Fragment / Heme-Peptide Fragment


Mass: 1007.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: tryptic cleavage product / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 458 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG 1900 MME , 0.1 M HEPES pH 7.5 , 0.2 M NaCl, 2 mM ZnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2009
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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→91.894 Å / Num. obs: 41019 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.5 / Num. measured all: 42171 / Num. unique all: 11639 / Rsym value: 0.308 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30.66 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.856 / SU B: 4.724 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.156 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2936 7.2 %RANDOM
Rwork0.187 ---
all0.19 41079 --
obs0.19 41018 99.85 %-
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: 70.17 Å2 / Biso mean: 24.619 Å2 / Biso min: 10.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 241 439 4004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223667
X-RAY DIFFRACTIONr_angle_refined_deg0.9562.1235013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1045430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34926.463164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90615589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.51158
X-RAY DIFFRACTIONr_chiral_restr0.0680.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022828
X-RAY DIFFRACTIONr_nbd_refined0.1850.21857
X-RAY DIFFRACTIONr_nbtor_refined0.2750.22489
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2334
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.251
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1120.26
X-RAY DIFFRACTIONr_mcbond_it0.3821.52241
X-RAY DIFFRACTIONr_mcangle_it0.6323440
X-RAY DIFFRACTIONr_scbond_it1.26331646
X-RAY DIFFRACTIONr_scangle_it1.9114.51562
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A423MEDIUM POSITIONAL0.140.5
B423MEDIUM POSITIONAL0.20.5
C423MEDIUM POSITIONAL0.20.5
D423MEDIUM POSITIONAL0.140.5
A384LOOSE POSITIONAL0.565
B384LOOSE POSITIONAL0.645
C384LOOSE POSITIONAL0.635
D384LOOSE POSITIONAL0.75
A423MEDIUM THERMAL0.462
B423MEDIUM THERMAL0.342
C423MEDIUM THERMAL0.522
D423MEDIUM THERMAL0.262
A384LOOSE THERMAL1.4310
B384LOOSE THERMAL1.1910
C384LOOSE THERMAL1.3610
D384LOOSE THERMAL0.8510
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 215 -
Rwork0.215 2777 -
all-2992 -
obs--100 %
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)
12.2450.9279-1.37351.5031-0.65812.0429-0.00160.06710.0205-0.0225-0.00360.0338-0.08810.05140.0052-0.0243-0.0048-0.0181-0.07710-0.1135-68.0122.139-11.121
22.16940.01010.40821.17860.05011.80930.075-0.1743-0.12940.06890.0266-0.09240.01670.0387-0.1015-0.0639-0.01730.0271-0.06820.0001-0.0439-79.95514.66428.722
31.7139-0.36810.41484.13060.09332.11820.023-0.1008-0.02990.3175-0.0532-0.05790.07140.00270.0302-0.0795-0.0029-0.0237-0.04450.0156-0.1258-89.71451.30310.885
43.5965-0.35371.5042.3447-0.86692.4565-0.0765-0.03440.3818-0.0699-0.01250.0518-0.0092-0.12260.089-0.0017-0.01210.0477-0.05040.0001-0.0125-87.3240.54834.671
514.20110.436912.457110.84752.618630.0844-1.05910.25290.130.53640.3482-1.0433-0.40572.38270.711-0.0906-0.04750.0060.06550.01340.0557-64.81219.43723.164
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 DIFFRACTION5E95 - 102

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