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- PDB-1ci3: CYTOCHROME F FROM THE B6F COMPLEX OF PHORMIDIUM LAMINOSUM -

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Basic information

Entry
Database: PDB / ID: 1ci3
TitleCYTOCHROME F FROM THE B6F COMPLEX OF PHORMIDIUM LAMINOSUM
ComponentsPROTEIN (CYTOCHROME F)
KeywordsELECTRON TRANSPORT / ELECTRON TRANSFER PROTEIN / COMPLEX SUBUNIT
Function / homology
Function and homology information


plasma membrane-derived 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 speciesPhormidium laminosum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCarrell, C.J. / Schlarb, B.G. / Howe, C.J. / Bendall, D.S. / Cramer, W.A. / Smith, J.L.
Citation
Journal: Biochemistry / Year: 1999
Title: Structure of the soluble domain of cytochrome f from the cyanobacterium Phormidium laminosum.
Authors: Carrell, C.J. / Schlarb, B.G. / Bendall, D.S. / Howe, C.J. / Cramer, W.A. / Smith, J.L.
#1: Journal: Protein Sci. / Year: 1996
Title: The Heme Redox Center of Chloroplast Cytochrome F is Linked to a Buried Five- Water Chain
Authors: Martinez, S.E. / Huang, D. / Ponomarev, M. / Cramer, W.A. / Smith, J.L.
History
DepositionApr 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 11, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / 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_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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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 2.1Aug 9, 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_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 2.2Nov 6, 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
M: PROTEIN (CYTOCHROME F)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2124
Polymers26,4631
Non-polymers7493
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: PROTEIN (CYTOCHROME F)
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)163,27124
Polymers158,7756
Non-polymers4,49618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_676x-y+1,-y+2,-z+11
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
Buried area14310 Å2
ΔGint-607 kcal/mol
Surface area69390 Å2
MethodPISA
3
M: PROTEIN (CYTOCHROME F)
hetero molecules

M: PROTEIN (CYTOCHROME F)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4248
Polymers52,9252
Non-polymers1,4996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)109.600, 109.600, 145.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein PROTEIN (CYTOCHROME F)


Mass: 26462.555 Da / Num. of mol.: 1 / Fragment: SOLUBLE EXTRINSIC FRAGMENT
Source method: isolated from a genetically manipulated source
Details: THIOETHER LINK BETWEEN CYS 21 AND HEME 254; COORDINATION OF HEME IRON BY HIS 25 AND N-TERMINAL AMINO GROUP
Source: (gene. exp.) Phormidium laminosum (bacteria) / Cellular location: MEMBRANE-CYTOPLASM INTERFACE / Gene: PETA / Plasmid: PUC19CF / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P95522
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HEC / HEME C


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


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.1 Å3/Da / Density % sol: 61.15 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMTris1drop
350 mM1dropNaCl
4100 mMMES1reservoir
5200 mMzinc acetate1reservoir
68-12 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 26071 / % possible obs: 97.9 % / Redundancy: 4.8 % / Rsym value: 3.2 / Net I/σ(I): 42
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 8.5 / Rsym value: 12.8 / % possible all: 83.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40 Å / % possible obs: 97.9 % / Redundancy: 4.8 % / Num. measured all: 126348 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 83.8 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 8.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HCZ

1hcz


Resolution: 1.9→30 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1993 8 %RANDOM
Rwork0.203 ---
obs-25589 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 120 Å2 / ksol: 1 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.81 Å2-1.35 Å20 Å2
2---1.81 Å20 Å2
3---3.629 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 45 250 2159
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.7
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_it1.23
X-RAY DIFFRACTIONx_mcangle_it1.834
X-RAY DIFFRACTIONx_scbond_it1.834
X-RAY DIFFRACTIONx_scangle_it2.665
LS refinement shellResolution: 1.9→1.92 Å / Total num. of bins used: 39
RfactorNum. reflection% reflection
Rfree0.288 19 6 %
Rwork0.233 308 -
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / Rfactor Rwork: 0.233

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