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- PDB-4jcg: Recombinant wild type Nitrosomonas europaea cytochrome c552 -

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Basic information

Entry
Database: PDB / ID: 4jcg
TitleRecombinant wild type Nitrosomonas europaea cytochrome c552
ComponentsCytochrome c-552
KeywordsELECTRON TRANSPORT / cytC domain / heme
Function / homology
Function and homology information


periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class ID / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c-552
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsWedekind, J.E. / Can, M. / Krucinska, J. / Bren, K.L.
CitationJournal: Chembiochem / Year: 2013
Title: Structural Characterization of Nitrosomonas europaea Cytochrome c-552 Variants with Marked Differences in Electronic Structure.
Authors: Can, M. / Krucinska, J. / Zoppellaro, G. / Andersen, N.H. / Wedekind, J.E. / Hersleth, H.P. / Andersson, K.K. / Bren, K.L.
History
DepositionFeb 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: 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_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.358, 60.358, 109.133
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-229-

HOH

21A-300-

HOH

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Components

#1: Protein Cytochrome c-552 / Cytochrome c-551 / Cytochrome c552


Mass: 8491.702 Da / Num. of mol.: 1 / Fragment: Cyt C552 (UNP Residues 23-103)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria)
Strain: ATCC 19718 / NBRC 14298 / Gene: cyt, cyt_c552, NE0102 / Plasmid: pSNEC, pEC86 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95339
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 19% (w/v) PEG 6000, 0.2 M LiCl, 0.1 M Tris-HCl pH 7.4 at 7-8 mM protein concentration., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: 2008 / Details: Rh coated Si mirrors; capillary microfocus
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.63→26.409 Å / Num. obs: 27203 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.04 / Net I/σ(I): 37.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 351C

351c


Resolution: 1.63→26.409 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): -3 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1365 5.02 %random
Rwork0.198 ---
all0.1998 ---
obs0.1998 27203 97.97 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.63→26.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms595 0 43 138 776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016672
X-RAY DIFFRACTIONf_angle_d1.63930
X-RAY DIFFRACTIONf_dihedral_angle_d14.563236
X-RAY DIFFRACTIONf_chiral_restr0.09797
X-RAY DIFFRACTIONf_plane_restr0.009116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.68820.29961260.25052179X-RAY DIFFRACTION83
1.6882-1.75580.2391380.23412589X-RAY DIFFRACTION99
1.7558-1.83570.25311430.24062644X-RAY DIFFRACTION100
1.8357-1.93240.2341380.21632628X-RAY DIFFRACTION100
1.9324-2.05350.26141360.21682635X-RAY DIFFRACTION100
2.0535-2.21190.23811370.19762631X-RAY DIFFRACTION100
2.2119-2.43440.22821400.20892656X-RAY DIFFRACTION100
2.4344-2.78630.29251360.20482620X-RAY DIFFRACTION100
2.7863-3.50920.20721360.18842656X-RAY DIFFRACTION100
3.5092-26.41250.21911350.17812600X-RAY DIFFRACTION98
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)
16.69550.36913.5339.1161-1.39743.8779-0.06870.971-0.2199-0.26490.14331.02670.1197-0.6886-0.07080.1912-0.00590.02130.7086-0.08990.4567-21.2426-22.3489-3.0711
23.8617-2.3454-3.11381.87991.42412.98820.11851.6351-0.6254-0.4181-0.4880.43250.0923-1.12650.31950.31570.04950.08010.7798-0.15410.3793-10.5436-25.004-10.1188
36.8113-3.00090.60766.31082.04535.9118-0.7957-1.3983-0.95081.14840.4251-0.10641.15780.65720.14150.5250.22430.20840.54060.18430.53820.1818-29.73253.4508
42.4712-0.4022-2.50640.14420.58312.93080.37590.150.4414-0.1421-0.1618-0.1579-0.48620.0822-0.2280.2240.04430.11430.23890.04340.2568-5.4014-16.8614-2.9527
53.5279-3.7807-0.16336.69391.44866.2246-0.28750.3877-1.06340.0837-0.10250.41180.4732-0.1860.32120.2019-0.04320.14290.2594-0.06960.3945-12.4125-26.27351.3839
60.12040.27110.0740.64160.30110.62490.24770.79540.5206-0.2894-0.2445-0.2545-0.3075-0.49840.00910.20890.12320.07240.41160.07120.2054-7.4955-18.8007-6.9129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:7)
2X-RAY DIFFRACTION2chain 'A' and (resseq 8:31)
3X-RAY DIFFRACTION3chain 'A' and (resseq 32:37)
4X-RAY DIFFRACTION4chain 'A' and (resseq 38:66)
5X-RAY DIFFRACTION5chain 'A' and (resseq 67:81)
6X-RAY DIFFRACTION6chain 'A' and (resseq 101:101

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