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- PDB-1ctm: CRYSTAL STRUCTURE OF CHLOROPLAST CYTOCHROME F REVEALS A NOVEL CYT... -

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Basic information

Entry
Database: PDB / ID: 1ctm
TitleCRYSTAL STRUCTURE OF CHLOROPLAST CYTOCHROME F REVEALS A NOVEL CYTOCHROME FOLD AND UNEXPECTED HEME LIGATION
ComponentsCYTOCHROME F
KeywordsELECTRON TRANSPORT(CYTOCHROME)
Function / homology
Function and homology information


chloroplast thylakoid membrane / photosynthesis / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rudiment single hybrid motif ...Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rudiment single hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
HEME C / Cytochrome f
Similarity search - Component
Biological speciesBrassica rapa (field mustard)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMartinez, S.E. / Huang, D. / Szczepaniak, A. / Cramer, W.A. / Smith, J.L.
Citation
Journal: Structure / Year: 1994
Title: Crystal structure of chloroplast cytochrome f reveals a novel cytochrome fold and unexpected heme ligation.
Authors: Martinez, S.E. / Huang, D. / Szczepaniak, A. / Cramer, W.A. / Smith, J.L.
History
DepositionJan 2, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650HELIX ALL HELICES ARE IN THE LARGE DOMAIN ONLY AND ARE DENOTED BY A LETTER ONLY.
Remark 700SHEET STRAND 3 OF SHEET SDA AND STRAND 3 OF SHEET SDB ARE PARTS OF A PIECE OF EXTENDED CHAIN WHICH ...SHEET STRAND 3 OF SHEET SDA AND STRAND 3 OF SHEET SDB ARE PARTS OF A PIECE OF EXTENDED CHAIN WHICH IS SPLIT BETWEEN BETWEEN THE TWO SHEETS. RESIDUES 176 - 179 BELONG TO SHEET SDA AND RESIDUES 181 - 185 BELONG TO SHEET SDB WITH A KINK IN BETWEEN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9372
Polymers27,3181
Non-polymers6191
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.200, 81.900, 46.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 117

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Components

#1: Protein CYTOCHROME F


Mass: 27318.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica rapa (field mustard) / References: UniProt: P36438
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE PRESENTED IN THIS ENTRY HAS NOT BEEN DEPOSITED IN THE SEQUENCE DATABASES. IT IS ...THE SEQUENCE PRESENTED IN THIS ENTRY HAS NOT BEEN DEPOSITED IN THE SEQUENCE DATABASES. IT IS DESCRIBED IN THE *JRNL* ARTICLE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 13189 / % possible obs: 94.7 % / Num. measured all: 52944 / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→6 Å / σ(F): 1
RfactorNum. reflection
Rfree0.277 -
Rwork0.198 -
obs0.198 10903
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 43 113 2081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.99
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Num. reflection obs: 10903 / σ(F): 1 / Rfactor obs: 0.198 / Rfactor Rfree: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.99

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