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- PDB-1m6z: Crystal structure of reduced recombinant cytochrome c4 from Pseud... -

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Basic information

Entry
Database: PDB / ID: 1m6z
TitleCrystal structure of reduced recombinant cytochrome c4 from Pseudomonas stutzeri
ComponentsCytochrome c4
KeywordsELECTRON TRANSPORT / diheme protein
Function / homology
Function and homology information


periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c4-like / : / 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 c4
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsNoergaard, A. / Harris, P. / Larsen, S. / Christensen, H.E.M.
Citation
Journal: To be Published
Title: Structural comparison of recombinant Pseudomonas stutzeri cytochrome c4 in two oxidation states
Authors: Noergaard, A. / Harris, P. / Larsen, S. / Christensen, H.E.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Crystallization and preliminary crystallographic investigations of cytochrome c4 from Pseudomonas stutzeri
Authors: Kadziola, A. / Larsen, S. / Christensen, H.M. / Karlsson, J.-J. / Ulstrup, J.
#2: Journal: Structure / Year: 1997
Title: Crystal structure of the dihaem cytochrome c4 from Pseudomonas stutzeri determined at 2.2 A resolution
Authors: Kadziola, A. / Larsen, S.
#3: Journal: HANDBOOK OF METALLOPROTEINS / Year: 2001
Title: Cytochrome c4
Authors: Andersen, N.H. / Christensen, H.E.M. / Iversen, G. / Noergaard, A. / Scharnagl, C. / Thuesen, M.H. / Ulstrup, J.
History
DepositionJul 18, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 25, 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_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 1.5Oct 16, 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 c4
B: Cytochrome c4
C: Cytochrome c4
D: Cytochrome c4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,05515
Polymers78,8004
Non-polymers5,25411
Water12,484693
1
A: Cytochrome c4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0294
Polymers19,7001
Non-polymers1,3293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9373
Polymers19,7001
Non-polymers1,2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0294
Polymers19,7001
Non-polymers1,3293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome c4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0594
Polymers19,7001
Non-polymers1,3593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.11, 57.56, 83.75
Angle α, β, γ (deg.)90.00, 104.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytochrome c4


Mass: 19700.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Plasmid: pNM185 / Production host: Pseudomonas putida (bacteria) / Strain (production host): PaW340 / References: UniProt: Q52369
#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 1.75 Å3/Da / Density % sol: 29.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.2M ammonium acetate, 0.1M sodium citrate pH 5.6, 30%(w/v) PEG 4000, 5%(v/v) glycerol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0326 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 26, 2001 / Details: Mirror
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0326 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 144067 / Num. obs: 142653 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.35→1.4 Å / % possible all: 87

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ETP

1etp


Resolution: 1.35→30 Å / Num. parameters: 59868 / Num. restraintsaints: 87330 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Anisotropic refinement. Riding H-atoms introduced.
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 7157 5.1 %RANDOM
Rwork0.1402 ---
all0.1427 141227 --
obs0.1427 130776 92.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 5369.27 / Occupancy sum non hydrogen: 6570.54
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5512 0 364 693 6569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0.445
X-RAY DIFFRACTIONs_from_restr_planes0.0263
X-RAY DIFFRACTIONs_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.084

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