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- PDB-1cno: STRUCTURE OF PSEUDOMONAS NAUTICA CYTOCHROME C552, BY MAD METHOD -

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Basic information

Entry
Database: PDB / ID: 1cno
TitleSTRUCTURE OF PSEUDOMONAS NAUTICA CYTOCHROME C552, BY MAD METHOD
ComponentsCYTOCHROME C552
KeywordsELECTRON TRANSPORT / PSEUDOMONAS NAUTICA / X RAY STRUCTURE / MULTIWAVELENGTH ANOMALOUS DISPERSION / HEME / CYTOCHROME C
Function / homology
Function and homology information


periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
: / 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 speciesMarinobacter hydrocarbonoclasticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsBrown, K. / Nurizzo, D. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: MAD structure of Pseudomonas nautica dimeric cytochrome c552 mimicks the c4 Dihemic cytochrome domain association.
Authors: Brown, K. / Nurizzo, D. / Besson, S. / Shepard, W. / Moura, J. / Moura, I. / Tegoni, M. / Cambillau, C.
History
DepositionAug 3, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_conn_type / 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_database_status.process_site / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C552
B: CYTOCHROME C552
C: CYTOCHROME C552
D: CYTOCHROME C552
E: CYTOCHROME C552
F: CYTOCHROME C552
G: CYTOCHROME C552
H: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,91019
Polymers69,6868
Non-polymers5,22411
Water13,115728
1
A: CYTOCHROME C552
B: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6584
Polymers17,4212
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-57 kcal/mol
Surface area7790 Å2
MethodPISA
2
C: CYTOCHROME C552
D: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6584
Polymers17,4212
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-54 kcal/mol
Surface area7900 Å2
MethodPISA
3
E: CYTOCHROME C552
F: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9357
Polymers17,4212
Non-polymers1,5135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-54 kcal/mol
Surface area7750 Å2
MethodPISA
4
G: CYTOCHROME C552
H: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6584
Polymers17,4212
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-55 kcal/mol
Surface area7930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.800, 121.800, 136.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11F-294-

HOH

21G-297-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.95569, -0.284576, 0.075316), (-0.286032, 0.958177, -0.009077), (-0.069583, -0.030218, -0.997118)11.82894, 5.23245, 117.60955
2given(-0.974396, -0.135802, 0.179192), (0.145224, -0.98857, 0.040489), (0.171645, 0.065475, 0.982981)3.3046, 63.94316, -4.29454
3given(-0.796097, -0.352278, -0.492067), (-0.363452, 0.928452, -0.076676), (0.483872, 0.117801, -0.867174)52.6272, -16.57082, 101.27085

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Components

#1: Protein
CYTOCHROME C552


Mass: 8710.734 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: C HEME IN EACH MONOMER LINKED BY CYS 14 AND 17 AND HIS 18 AND MET 60 AS AXIAL LIGANDS
Source: (natural) Marinobacter hydrocarbonoclasticus (bacteria)
Cellular location: PERIPLASM / Strain: 617 / References: UniProt: P82903
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE 3 C-TERMINAL SIDE CHAINS WERE NOT SEEN IN THE DENSITY MAP AND WERE REPLACED BY ALANINE. LEU 36 ...THE 3 C-TERMINAL SIDE CHAINS WERE NOT SEEN IN THE DENSITY MAP AND WERE REPLACED BY ALANINE. LEU 36 CHANGED TO LYS 36; GLY 79 CHANGED TO TYR 79 COMPARED TO REF. EURO. J. BIOL. (1994), 224, 1011-1017.

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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: 4.36 Å3/Da / Density % sol: 72 %
Description: THE STARTING MODEL WAS THE C552 FROM PS. NAUTICA SOLVED BY MAD METHOD AT 2.8A RESOLUTION
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 Mammonium sulfate1reservoir
2100 mMsodium citrate1reservoirpH5.6
312 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.756
DetectorType: THOMPSON
Detector: X RAY IMAGE INTENSIFIER (THOMPSON) + PRINCETON CCD DETECTOR
Date: May 1, 1998 / Details: FOCUSED BEAM TOROIDAL
RadiationMonochromator: LAUE BRAGG / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.756 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 58183 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 18.84 Å2 / Rsym value: 0.108 / Net I/σ(I): 6.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.246 / % possible all: 94.3
Reflection
*PLUS
Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Rmerge(I) obs: 0.229

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
PROWdata reduction
CCP4(SCALA)data scaling
X-PLOR3.843phasing
RefinementResolution: 2.2→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 400000 / Data cutoff low absF: 1.0E-5 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1708 3 %RANDOM
Rwork0.1784 ---
obs0.1784 58148 99.31 %-
Displacement parametersBiso mean: 19.26 Å2
Refine analyzeLuzzati d res low obs: 2.2 Å / Luzzati sigma a obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4846 0 362 728 5936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.269
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.59
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.841
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2374 220 3.02 %
Rwork0.2073 6730 -
obs--95.41 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2083
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.267 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.593
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.841

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