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- PDB-1e2w: N168F mutant of cytochrome f from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 1e2w
TitleN168F mutant of cytochrome f from Chlamydomonas reinhardtii
ComponentsCYTOCHROME F
KeywordsELECTRON TRANSPORT PROTEINS / INTERNAL WATER CHAIN / PHOTOSYNTHETIC FUNCTION IMPAIRED
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 speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSainz, G. / Carrell, C.J. / Ponamarev, M.V. / Soriano, G.M. / Cramer, W.A. / Smith, J.L.
CitationJournal: Biochemistry / Year: 2000
Title: Interruption of the Internal Water Chain of Cytochrome F Impairs Photosynthetic Function
Authors: Sainz, G. / Carrell, C.J. / Ponamarev, M.V. / Soriano, G.M. / Cramer, W.A. / Smith, J.L.
History
DepositionMay 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 6, 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 / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6674
Polymers54,4302
Non-polymers1,2372
Water13,637757
1
A: CYTOCHROME F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8342
Polymers27,2151
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8342
Polymers27,2151
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.030, 81.180, 61.080
Angle α, β, γ (deg.)90.00, 103.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYTOCHROME F


Mass: 27215.033 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Gene: PETA / Plasmid: PUCPF2 / Gene (production host): CCMABCDEFGH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MV1190 / References: UniProt: P23577
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 757 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C ENGINEERED MUTATION ASN168PHE. ONLY THE SOLUBLE DOMAIN OF THE MATURE MEMBRANE PROTEIN ...CHAIN A, B, C ENGINEERED MUTATION ASN168PHE. ONLY THE SOLUBLE DOMAIN OF THE MATURE MEMBRANE PROTEIN WAS EXPRESSED AND CRYSTALLIZED (251 A.A. OF 317 A.A.). 31-RESIDUE PRE-SEQUENCE IS A THYLAKOID IMPORT SIGNAL C-TERMINAL 35-RESIDUES ARE THE MEMBRANE ANCHOR. BOTH WERE EXCLUDED FROM THE EXPRESSED CONSTRUCT.
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: 2.62 Å3/Da / Density % sol: 52.6 %
Crystal growpH: 6.7
Details: THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, PH 7.5, 1 MM DTT, THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 200 MM AMMONIUM FORMATE, 14% GLYCEROL, 17% PEG-3350.
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21 mMdithiothreitol1drop
3100 mMMES1reservoir
4200 mMammonium formate1reservoir
514 %glycerol1reservoir
617 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.6526
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 15, 1999 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6526 Å / Relative weight: 1
ReflectionResolution: 1.6→27.84 Å / Num. obs: 73580 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 28.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.54 / Rsym value: 0.378 / % possible all: 100
Reflection
*PLUS
Num. measured all: 277890
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E2V

1e2v


Resolution: 1.6→27.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1175031.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE LOOP 186-190 IS BADLY DEFINED IN THE ELECTRON DENSITY. ONLY THE MAIN CHAIN OF THE ARG 251 WAS SEEN IN THE ELCTRON DENSITY MAP FOR THE B CHAIN , SO AN ALA 251 WAS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3704 5.2 %RANDOM
Rwork0.197 ---
obs0.197 71219 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4172 Å2 / ksol: 0.359825 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å21.76 Å2
2---0.58 Å20 Å2
3----0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-27.84 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 86 757 4675
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.291.5
X-RAY DIFFRACTIONc_mcangle_it3.772
X-RAY DIFFRACTIONc_scbond_it4.352
X-RAY DIFFRACTIONc_scangle_it6.662.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 578 5.2 %
Rwork0.246 10541 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM19X.HEMETOPH19CNS.HEME
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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