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Basic information

Entry
Database: PDB / ID: 3hni
TitleCrystal structure of the Zn-induced tetramer of the engineered cyt cb562 variant RIDC-1
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Electron 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: 2.35 Å
AuthorsSalgado, E.N. / Lewis, R.A. / Brodin, J. / Tezcan, F.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Metal templated design of protein interfaces.
Authors: Salgado, E.N. / Ambroggio, X.I. / Brodin, J.D. / Lewis, R.A. / Kuhlman, B. / Tezcan, F.A.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 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.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

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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)99,04824
Polymers93,5938
Non-polymers5,45516
Water2,468137
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)49,52412
Polymers46,7964
Non-polymers2,7288
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-264 kcal/mol
Surface area18630 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)49,52412
Polymers46,7964
Non-polymers2,7288
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-265 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.208, 87.935, 152.174
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

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Components

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


Mass: 11699.084 Da / Num. of mol.: 8 / Mutation: R34A, L38A, Q41W, K42S, D66W, V69I
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.: 137 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES, 30% Jeffamine ED-2001, 1.5 mM zinc chloride, pH 7, 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: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 23, 2008
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→45.74 Å / Num. all: 32669 / Num. obs: 32114 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 5.3
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.4 / Num. measured all: 8350 / Num. unique all: 4497 / Rsym value: 0.55 / % possible all: 96

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QLA

2qla


Resolution: 2.35→45.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.747 / SU B: 18.837 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.219 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2296 7.2 %RANDOM
Rwork0.226 ---
obs0.229 32072 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 50.38 Å2 / Biso mean: 32.045 Å2 / Biso min: 8.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.35→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 352 137 7033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227156
X-RAY DIFFRACTIONr_angle_refined_deg1.2832.0879770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6365840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.75426.486333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.843151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9131516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025506
X-RAY DIFFRACTIONr_nbd_refined0.2130.23610
X-RAY DIFFRACTIONr_nbtor_refined0.2830.24812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2208
X-RAY DIFFRACTIONr_metal_ion_refined0.080.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.213
X-RAY DIFFRACTIONr_mcbond_it0.3841.54359
X-RAY DIFFRACTIONr_mcangle_it0.71926751
X-RAY DIFFRACTIONr_scbond_it1.42633225
X-RAY DIFFRACTIONr_scangle_it2.1384.53003
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A424TIGHT POSITIONAL0.050.05
B424TIGHT POSITIONAL0.060.05
C424TIGHT POSITIONAL0.040.05
D424TIGHT POSITIONAL0.050.05
E424TIGHT POSITIONAL0.050.05
F424TIGHT POSITIONAL0.050.05
G424TIGHT POSITIONAL0.040.05
H424TIGHT POSITIONAL0.050.05
A376LOOSE POSITIONAL0.675
B376LOOSE POSITIONAL0.635
C376LOOSE POSITIONAL0.675
D376LOOSE POSITIONAL0.625
E376LOOSE POSITIONAL0.745
F376LOOSE POSITIONAL0.785
G376LOOSE POSITIONAL0.685
H376LOOSE POSITIONAL0.725
A424TIGHT THERMAL0.070.5
B424TIGHT THERMAL0.080.5
C424TIGHT THERMAL0.060.5
D424TIGHT THERMAL0.080.5
E424TIGHT THERMAL0.080.5
F424TIGHT THERMAL0.080.5
G424TIGHT THERMAL0.070.5
H424TIGHT THERMAL0.080.5
A376LOOSE THERMAL1.1710
B376LOOSE THERMAL1.5810
C376LOOSE THERMAL1.2910
D376LOOSE THERMAL1.3710
E376LOOSE THERMAL1.3410
F376LOOSE THERMAL1.510
G376LOOSE THERMAL1.310
H376LOOSE THERMAL1.3710
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 154 -
Rwork0.295 2103 -
all-2257 -
obs--94.4 %
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)
11.55350.4130.17928.5230.99563.51010.1656-0.3447-0.16610.1568-0.2652-0.2547-0.04970.01020.0996-0.1363-0.0815-0.0103-0.02460.0377-0.1533-23.96321.232-4.269
23.3061-1.17360.19827.79620.47721.43310.0933-0.0634-0.2735-0.2786-0.0927-0.32180.12310.2532-0.0006-0.1714-0.00590.0294-0.06090.0591-0.14-7.57222.139-20.037
33.3681-0.0007-1.15075.8397-0.89085.69930.27940.5445-0.1362-0.0663-0.17730.2134-0.4292-0.4391-0.1022-0.00250.1293-0.04160.0288-0.0766-0.1757-21.75519.31-33.881
44.10671.3381-0.30134.4086-0.64292.34020.0680.054-0.23580.0381-0.05650.20520.2587-0.3969-0.0115-0.1887-0.0258-0.0325-0.0269-0.0531-0.1237-37.00525.923-18.556
50.98710.5512-0.0146.70252.13833.31110.02370.25380.1111-0.1889-0.0892-0.3027-0.2638-0.08230.0655-0.0940.0614-0.0034-0.04620.0303-0.13554.26220.95-72.126
63.8434-1.97260.61964.936-0.76872.32370.0673-0.06730.2178-0.0999-0.08370.1484-0.223-0.29890.0164-0.19080.0220.0367-0.0223-0.0533-0.143-8.416.38-57.525
72.46730.0838-0.05034.34790.09244.75010.2211-0.39950.04370.1889-0.21280.23390.1846-0.2272-0.0082-0.0146-0.1190.01710.0179-0.0466-0.1447.00223.164-42.451
83.48730.7743-0.93427.2777-0.49951.6910.0505-0.15240.22070.2717-0.1051-0.334-0.27570.29720.0545-0.1518-0.0108-0.0373-0.05830.0448-0.136321.03420.257-56.404
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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