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- PDB-1ql3: Structure of the soluble domain of cytochrome c552 from Paracoccu... -

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Basic information

Entry
Database: PDB / ID: 1ql3
TitleStructure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the reduced state
ComponentsCYTOCHROME C552
KeywordsELECTRON TRANSPORT PROTEIN (CYTOCHROME) / ELECTRON TRANSFER / REDUCED
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c, class IA/ IB / 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 speciesPARACOCCUS DENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å
AuthorsHarrenga, A. / Reincke, B. / Rueterjans, H. / Ludwig, B. / Michel, H.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structure of the Soluble Domain of Cytochrome C552 from Paracoccus Denitrificans in the Oxidized and Reduced States
Authors: Harrenga, A. / Reincke, B. / Rueterjans, H. / Ludwig, B. / Michel, H.
History
DepositionAug 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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_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

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Assembly

Deposited unit
A: CYTOCHROME C552
B: CYTOCHROME C552
C: CYTOCHROME C552
D: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1658
Polymers41,6914
Non-polymers2,4744
Water10,449580
1
A: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0412
Polymers10,4231
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0412
Polymers10,4231
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0412
Polymers10,4231
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0412
Polymers10,4231
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.690, 54.320, 140.740
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 C552


Mass: 10422.782 Da / Num. of mol.: 4 / Fragment: SOLUBLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: MEMBRANE-BOUND / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P54820
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.47 Å3/Da / Density % sol: 49.7 %
Crystal growpH: 4.5 / Details: pH 4.50
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMcytochrome1drop
210 mMTris-HCl1drop
320 mM1dropNaCl
450 mMsodium acetate1reservoir
520.0-22.5 %PEG15001reservoir
610 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9059
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9059 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 80254 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 30.9
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 8.4 / % possible all: 98
Reflection
*PLUS
Num. measured all: 277074
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.4→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 8020 10 %RANDOM
Rwork0.208 ---
obs0.208 80070 98 %-
Solvent computationSolvent model: USED
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2---4.56 Å20 Å2
3---2.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 172 580 3680
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.43
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.961.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.52.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 1257 9.9 %
Rwork0.296 11465 -
obs--94.4 %
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.43

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