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- PDB-1ft5: CRYSTAL STRUCTURE OF THE OXIDIZED STATE OF CYTOCHROME C554 FROM N... -

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Basic information

Entry
Database: PDB / ID: 1ft5
TitleCRYSTAL STRUCTURE OF THE OXIDIZED STATE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA
ComponentsCYTOCHROME C554
KeywordsELECTRON TRANSPORT / heme-stacking
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
: / Cytochrome c-552/4 / Cytochrome c554 and c-prime / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Cytochrome c-554
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsIverson, T.M. / Arciero, D.M. / Hooper, A.B. / Rees, D.C.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2001
Title: High-resolution structures of the oxidized and reduced states of cytochrome c554 from Nitrosomonas europaea.
Authors: Iverson, T.M. / Arciero, D.M. / Hooper, A.B. / Rees, D.C.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Heme Packing Motifs Revealed by the Crystal Structure of the Tetra-heme Cytochrome c554 from Nitrosomonas europaea
Authors: Iverson, T.M. / Arciero, D.M. / Hsu, B.T. / Logan, M.S. / Hooper, A.B. / Rees, D.C.
History
DepositionSep 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Oct 16, 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 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C554
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4088
Polymers23,6571
Non-polymers2,7517
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.892, 147.892, 33.913
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein CYTOCHROME C554 / C554 / HYDROXYLAMINE OXIDOREDUCTASE-LINKED CYTOCHROME


Mass: 23656.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHEMOAUTOTROPHIC BACTERIUM INVOLVED IN BIOLOGICAL NITRIFICATION
Source: (natural) Nitrosomonas europaea (bacteria) / References: UniProt: Q57142
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10.1
Details: 62.5% w/vol potassium phosphate pH 10.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Details: Iverson, T.M., (1998) Nat.Struct.Biol., 5, 1005.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
262.5 %(w/v)potassium phosphate1reservoirpH10.1
392.5 %(w/v)potassium phosphate1reservoirpH10.1

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 109601 / Num. obs: 35562 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.08 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 28
Reflection shellResolution: 1.6→1.68 Å / Rmerge(I) obs: 0.174 / % possible all: 86.1
Reflection
*PLUS
Num. measured all: 109601
Reflection shell
*PLUS
% possible obs: 86.1 % / Mean I/σ(I) obs: 7.3

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Processing

Software
NameClassification
X-PLORrefinement
REFMACrefinement
AMoREphasing
SHELXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.215 1808 random
Rwork0.188 --
all-109601 -
obs-35562 -
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 187 142 1988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.99
X-RAY DIFFRACTIONx_bond_d0.021
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg

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