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- PDB-1e2v: N153Q mutant of cytochrome f from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 1e2v
TitleN153Q mutant of cytochrome f from Chlamydomonas reinhardtii
ComponentsCYTOCHROME F
KeywordsELECTRON TRANSPORT / 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) / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / HEME C / Cytochrome f
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 29, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2000Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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

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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)83,6219
Polymers81,5883
Non-polymers2,0336
Water21,3661186
1
A: CYTOCHROME F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9334
Polymers27,1961
Non-polymers7373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8743
Polymers27,1961
Non-polymers6782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CYTOCHROME F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8142
Polymers27,1961
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.120, 94.220, 121.080
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: 27195.988 Da / Num. of mol.: 3 / 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 / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1186 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C ENGINEERED MUTATION ASN153GLN. ONLY THE SOLUBLE DOMAIN OF THE MATURE MEMBRANE PROTEIN ...CHAIN A, B, C ENGINEERED MUTATION ASN153GLN. 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.

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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: 2.66 Å3/Da / Density % sol: 53.43 %
Crystal growpH: 6.5
Details: THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 6.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.5, 25 MM CALCIUM ACETATE, 1 MM DTT AND 17-19% PEG 8000.
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 7.5 / Method: vapor diffusion / Details: temperature was changed to 20 degress after 4 days
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
280 mM1dropNa2HPO4/NaH2PO4
31 mMdithiothreitol1drop
4100 mMMES1reservoir
525 mMcalcium acetate1reservoir
61 mMdithiothreitol1reservoir
717-19 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→43.85 Å / Num. obs: 73484 / % possible obs: 97.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 26.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 3.73 / Rsym value: 0.305 / % possible all: 90.2
Reflection
*PLUS
Num. measured all: 329989
Reflection shell
*PLUS
% possible obs: 90.2 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EWH

1ewh


Resolution: 1.85→42.33 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2405744.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3635 5.1 %RANDOM
Rwork0.185 ---
obs0.185 71428 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.308 Å2 / ksol: 0.340713 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å20 Å2
2---2.01 Å20 Å2
3---4.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-43.85 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5751 0 141 1186 7078
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_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it2.422
X-RAY DIFFRACTIONc_scangle_it3.672.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 550 5.2 %
Rwork0.221 9951 -
obs--85.1 %
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
X-RAY DIFFRACTION5ACETATE.PARACETATE.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_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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