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- PDB-1cfm: CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII -

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Basic information

Entry
Database: PDB / ID: 1cfm
TitleCYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII
ComponentsCYTOCHROME F
KeywordsELECTRON TRANSPORT / CYTOCHROME F / PLASTOCYANIN / PROTON WIRE / HEME
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 speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChi, Y.I. / Huang, L.S. / Zhang, Z. / Fernandez-Velasco, J.G. / Malkin, R. / Berry, E.A.
CitationJournal: Biochemistry / Year: 2000
Title: X-ray structure of a truncated form of cytochrome f from chlamydomonas reinhardtii.
Authors: Chi, Y.I. / Huang, L.S. / Zhang, Z. / Fernandez-Velasco, J.G. / Berry, E.A.
History
DepositionSep 18, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME F
B: CYTOCHROME F
C: CYTOCHROME F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3956
Polymers81,5463
Non-polymers1,8493
Water18,0331001
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.624, 94.943, 119.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.8202, -0.1378, -0.5553), (0.1715, 0.9851, 0.0089), (0.5458, -0.1025, 0.8316)70.8511, -19.7688, 29.4244
2given(-0.411, 0.1419, 0.9005), (0.3186, 0.9479, -0.0039), (-0.8542, 0.2853, -0.4347)-35.273, 17.0216, 86.3696

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Components

#1: Protein CYTOCHROME F /


Mass: 27181.961 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: F283ST / References: UniProt: P23577
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 1001 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1180 g/LPEG80001reservoir
20.1 Msodium cacodylate1reservoir
30.2 M1reservoirZn(OAc)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28.6 Å / Num. obs: 47521 / % possible obs: 81.6 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.042 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.213 / % possible all: 71.5
Reflection
*PLUS
% possible obs: 91.6 % / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 68.7 % / Rmerge(I) obs: 0.176

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Processing

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

1ctm


Resolution: 2→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2304748.85 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: MLF - MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: NO NCS RESTRAINTS WERE USED IN FINAL REFINEMENT. DATA CUTOFF HIGH (ABS(F)) : 2304748.85 DATA CUTOFF LOW (ABS(F)) : 0.000000
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2346 5 %RANDOM
Rwork0.214 ---
obs0.214 46907 79.5 %-
Solvent computationSolvent model: CNS 0.1 BULK SOLVENT / Bsol: 53.9 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5745 0 129 1001 6875
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.642.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 362 5.4 %
Rwork0.241 6396 -
obs--69.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.P
X-RAY DIFFRACTION2PROTEIN_RETOPH19.RCV
X-RAY DIFFRACTION3PARHCSDX.PTOPH19X.HEME
X-RAY DIFFRACTION4PARAM19X.HEME
Software
*PLUS
Name: CNS / Version: 0.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.37

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