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- PDB-1hcz: LUMEN-SIDE DOMAIN OF REDUCED CYTOCHROME F AT-35 DEGREES CELSIUS -

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Basic information

Entry
Database: PDB / ID: 1hcz
TitleLUMEN-SIDE DOMAIN OF REDUCED CYTOCHROME F AT-35 DEGREES CELSIUS
ComponentsCYTOCHROME F
KeywordsELECTRON TRANSPORT / PHOTOSYNTHESIS / CYTOCHROME B6F COMPLEX / CHLOROPLAST TRANSMEMBRANE
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) / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome f
Similarity search - Component
Biological speciesBrassica rapa (field mustard)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.96 Å
AuthorsMartinez, S.E. / Huang, D. / Szczepaniak, A. / Cramer, W.A. / Smith, J.L.
Citation
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.
#1: 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
DepositionSep 18, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1622
Polymers27,5451
Non-polymers6161
Water7,350408
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.600, 82.200, 45.200
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 F


Mass: 27545.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica rapa (field mustard) / Organ: LEAF / Organelle: CHLOROPLAST / References: UniProt: P36438
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53 %
Crystal grow
*PLUS
Temperature: 5-9 ℃ / Method: capillary vapor diffusion method

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Data collection

DiffractionMean temperature: 238 K
Diffraction sourceWavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 21059 / % possible obs: 97.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.068
Reflection
*PLUS
Highest resolution: 1.96 Å / Num. measured all: 86869

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Processing

Software
NameVersionClassification
TNT5Arefinement
XDSdata reduction
RefinementMethod to determine structure: MIRAS / Highest resolution: 1.96 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.25 986 5 %RANDOM
Rwork0.158 ---
obs-19639 90 %-
Solvent computationSolvent model: TNT BULK SOLVENT CORRECTION / Bsol: 251.3 Å2 / ksol: 0.73 e/Å3
Refinement stepCycle: LAST / Highest resolution: 1.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 43 408 2375
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01320188
X-RAY DIFFRACTIONt_angle_deg1.5275410
X-RAY DIFFRACTIONt_dihedral_angle_d20.6131920
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle19.92220
X-RAY DIFFRACTIONt_trig_c_planes0.017599
X-RAY DIFFRACTIONt_gen_planes0.01728230
X-RAY DIFFRACTIONt_it4.618260.4
X-RAY DIFFRACTIONt_nbd0.0486420
Software
*PLUS
Name: TNT / Version: 5A / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.620
X-RAY DIFFRACTIONt_plane_restr0.01730

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