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- PDB-1tef: Crystal structure of the spinach plastocyanin mutants G8D/K30C/T6... -

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Basic information

Entry
Database: PDB / ID: 1tef
TitleCrystal structure of the spinach plastocyanin mutants G8D/K30C/T69C and K30C/T69C- a study of the effect on crystal packing and thermostability from the introduction of a novel disulfide bond
ComponentsPlastocyanin, chloroplast
KeywordsPHOTOSYNTHESIS / Plastocyanin / disulfide bond / mutant / blue copper protein
Function / homology
Function and homology information


chloroplast thylakoid membrane / electron transfer activity / copper ion binding
Similarity search - Function
Plastocyanin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Plastocyanin, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOkvist, M. / Jacobson, F. / Jansson, H. / Hansson, O. / Sjolin, L.
CitationJournal: To be Published
Title: Novel Disulfide Bonds Effect the Thermostability of Plastocyanin. Crystal structures of the triple plastocyanin mutant G8D/K30C/T69C and the double plastocyanin mutant K30C/T69C from spinach ...Title: Novel Disulfide Bonds Effect the Thermostability of Plastocyanin. Crystal structures of the triple plastocyanin mutant G8D/K30C/T69C and the double plastocyanin mutant K30C/T69C from spinach at 1.90 and 1.96 resolution, respectively.
Authors: Okvist, M. / Jacobson, F. / Jansson, H. / Hansson, O. / Sjolin, L.
History
DepositionMay 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 16, 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
A: Plastocyanin, chloroplast
B: Plastocyanin, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0725
Polymers20,9092
Non-polymers1633
Water3,585199
1
A: Plastocyanin, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5543
Polymers10,4551
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plastocyanin, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5182
Polymers10,4551
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.320, 52.320, 127.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-417-

HOH

21B-469-

HOH

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Components

#1: Protein Plastocyanin, chloroplast


Mass: 10454.595 Da / Num. of mol.: 2 / Mutation: G8D, K30C, T69C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: PETE / Plasmid: pUG101tr / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 / References: UniProt: P00289
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 21% PEG 3350, 0.25M MgCl2, 0.1M Na-acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.991 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 13, 2001
RadiationMonochromator: FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991 Å / Relative weight: 1
ReflectionResolution: 1.9→45.18 Å / Num. all: 16181 / Num. obs: 16181 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 53.62
Reflection shellResolution: 1.9→2.1 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.047 / Mean I/σ(I) obs: 38.05 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345data collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AG6

1ag6


Resolution: 1.9→19.2 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.539 / SU ML: 0.076 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20379 820 5.1 %RANDOM
Rwork0.15689 ---
obs0.15925 15359 98.05 %-
all-16181 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.133 Å0.139 Å
Luzzati sigma a-0.109 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 3 199 1668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211498
X-RAY DIFFRACTIONr_bond_other_d0.0020.021288
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9682032
X-RAY DIFFRACTIONr_angle_other_deg0.79933028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.71115246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02278
X-RAY DIFFRACTIONr_nbd_refined0.1930.2250
X-RAY DIFFRACTIONr_nbd_other0.2550.21459
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.2841
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2140
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0630.51
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9611.5976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75121560
X-RAY DIFFRACTIONr_scbond_it2.863522
X-RAY DIFFRACTIONr_scangle_it4.7224.5472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.198 57
Rwork0.146 1069

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