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- PDB-3zow: Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 -

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Basic information

Entry
Database: PDB / ID: 3zow
TitleCrystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552
ComponentsCYTOCHROME C-552
KeywordsELECTRON TRANSPORT / HEMEPROTEIN
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHersleth, H.-P. / Can, M. / Krucinska, J. / Zoppellaro, G. / Andersen, N.H. / Karlsen, S. / Wedekind, J.E. / Andersson, K.K. / 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 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _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_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

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Assembly

Deposited unit
A: CYTOCHROME C-552
B: CYTOCHROME C-552
C: CYTOCHROME C-552
D: CYTOCHROME C-552
E: CYTOCHROME C-552
F: CYTOCHROME C-552
G: CYTOCHROME C-552
H: CYTOCHROME C-552
I: CYTOCHROME C-552
J: CYTOCHROME C-552
K: CYTOCHROME C-552
L: CYTOCHROME C-552
M: CYTOCHROME C-552
N: CYTOCHROME C-552
O: CYTOCHROME C-552
P: CYTOCHROME C-552
Q: CYTOCHROME C-552
R: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,98436
Polymers152,85118
Non-polymers11,13318
Water3,891216
1
A: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
17
Q: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
18
R: CYTOCHROME C-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers8,4921
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.450, 137.930, 204.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CYTOCHROME C-552 / CYTOCHROME C-551 / CYTOCHROME C552


Mass: 8491.702 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) NITROSOMONAS EUROPAEA (bacteria)
References: UniProt: P95339, nitrite reductase (cytochrome; ammonia-forming)
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.57 Å3/Da / Density % sol: 51.9 % / Description: NONE
Crystal growpH: 8 / Details: 3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8496
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8496 Å / Relative weight: 1
ReflectionResolution: 2.35→38.8 Å / Num. obs: 68939 / % possible obs: 97.1 % / Observed criterion σ(I): 6 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZOX

3zox


Resolution: 2.35→35.22 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.891 / SU B: 13.213 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. IT IS COMMON IN PUBLICATIONS ETC. TO START THE NUMBERING OF THE CYTOCHROME C552 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. IT IS COMMON IN PUBLICATIONS ETC. TO START THE NUMBERING OF THE CYTOCHROME C552 NITROSOMONAS EUROPAEA WITH THE FIRST RESIDUE IN THE SEQUENCE BEING NUMBERED AS RESIDUE 3. SINGLE-CRYSTAL UV-VIS SPECTRA HAVE BEEN RECORDED BEFORE AND AFTER EXPOSURE TO X-RAYS SHOWING THE RADIATION-INFLUENCE OF THE FERRIC CYTOCHROME C552 CRYSTALS SEE JRNL.
RfactorNum. reflection% reflectionSelection details
Rfree0.25765 3487 5.1 %RANDOM
Rwork0.20115 ---
obs0.20406 65371 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.493 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---1.05 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.35→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10640 0 774 216 11630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211728
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9112.06316190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17851433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.35927.594374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.986151841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1270.21738
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218804
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0082.6375783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.233.9387199
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1752.7685945
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 225 -
Rwork0.289 4173 -
obs--85 %
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)
11.5176-0.15020.23281.149-0.26121.1553-0.016-0.00110.00750.08510.0610.02130.01830.0139-0.04490.0212-0.0012-0.00360.0443-0.00520.0485-3.139-25.2914.091
20.8545-0.4607-0.08380.45560.11.45240.0041-0.00820.0045-0.00130.0408-0.03920.01630.0008-0.0450.0152-0.001-0.00310.04290.00050.0752-26.002-26.13997.112
31.2436-0.06750.53191.1836-0.00521.24240.0002-0.02110.0042-0.0129-0.03340.0869-0.0564-0.08320.03320.0277-0.0035-0.02160.02250.00350.0889-17.849-56.54291.572
41.2676-0.2352-0.56650.775-0.04361.1054-0.0176-0.0318-0.06350.0719-0.059-0.02520.08170.03910.07660.06160.0136-0.01010.05160.00980.0274-44.935-40.04615.695
51.8272-0.0465-0.00221.5544-0.41270.9001-0.04270.03240.01630.02290.0374-0.0897-0.0076-0.01250.00530.00920.0091-0.02010.02810.0020.0915-31.196-16.1269.284
62.127-0.86512.86282.33460.17035.2138-0.21840.31710.3450.1468-0.1299-0.0620.06810.43390.34830.2474-0.0556-0.14910.1580.0720.1249-39.016-33.92544.717
71.2353-1.05780.92382.5365-0.35522.18010.0377-0.00740.08210.0727-0.0176-0.2444-0.0586-0.0114-0.020.03280.003-0.0340.0186-0.02360.0939-12.68-58.03913.146
81.7802-0.2935-0.1931.2838-0.2430.7417-0.02540.0028-0.0081-0.01380.03280.1214-0.0134-0.0158-0.00750.0217-0.0072-0.04180.02960.01060.092.942-17.82490.102
91.91820.13990.20551.1903-0.00261.49490.02380.1322-0.10450.0179-0.04580.10160.07260.00360.0220.02550.0064-0.01840.0158-0.01820.07930.391-0.1893.89
102.8617-1.43161.49073.4866-1.36941.28960.36870.0966-0.242-0.4599-0.25080.12850.32890.0403-0.11780.15920.0496-0.07330.0378-0.02780.0479-28.024-54.46669.852
111.31710.0917-0.07431.65470.41451.91510.00630.0168-0.1289-0.0716-0.00530.06470.0484-0.0377-0.0010.0194-0.0159-0.01790.033-0.01370.0733-43.25-43.17688.183
121.17650.1672-0.08962.68710.11231.25440.02450.0530.0531-0.1347-0.0865-0.1489-0.0242-0.04830.06190.0529-0.013-0.03190.03660.0370.0611-37.545-12.8378.055
131.7197-0.95990.58673.42250.9932.90870.12730.0972-0.00820.1716-0.13480.02520.1535-0.28340.00760.0723-0.0142-0.01910.09460.00540.0098-50.014-33.50465.629
141.13750.2146-0.35533.2856-1.17441.62330.07510.00850.18520.1980.0398-0.0634-0.08850.0406-0.11480.0779-0.014-0.01080.0191-0.00870.0526-49.516-11.52926.508
151.4215-0.04690.59982.0808-1.20412.6258-0.0002-0.18010.04590.28550.06520.0858-0.2691-0.2948-0.0650.07450.02120.01560.1378-0.03190.0172-8.795-22.72133.82
163.7448-4.49151.97129.8803-3.68071.61240.42960.67420.0014-0.2778-0.394-0.210.60840.2773-0.03571.16050.2105-0.23860.1721-0.04090.0593-33.088-56.08646.555
171.79710.3174-0.07163.42320.00370.87230.063-0.1831-0.0599-0.007-0.10620.00770.1838-0.07450.04320.1173-0.0791-0.01760.07310.01970.01180.5-43.67234.629
181.02560.9955-0.92384.79452.17483.426-0.148-0.12680.1317-0.43750.21820.2083-0.09190.5369-0.07020.04760.0114-0.02540.227-0.0240.0208-20.325-29.87267.871
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 81
2X-RAY DIFFRACTION2B1 - 81
3X-RAY DIFFRACTION3A1 - 81
4X-RAY DIFFRACTION4D1 - 81
5X-RAY DIFFRACTION5E1 - 81
6X-RAY DIFFRACTION6Q1 - 81
7X-RAY DIFFRACTION7G1 - 81
8X-RAY DIFFRACTION8H1 - 81
9X-RAY DIFFRACTION9I1 - 81
10X-RAY DIFFRACTION10J1 - 81
11X-RAY DIFFRACTION11K1 - 81
12X-RAY DIFFRACTION12L1 - 81
13X-RAY DIFFRACTION13P10 - 81
14X-RAY DIFFRACTION14N1 - 81
15X-RAY DIFFRACTION15M1 - 81
16X-RAY DIFFRACTION16R1 - 81
17X-RAY DIFFRACTION17O1 - 81
18X-RAY DIFFRACTION18F1 - 81

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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