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- PDB-2bz7: Oxidized and reduced structures of a mutant Plastocyanin of fern -

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Basic information

Entry
Database: PDB / ID: 2bz7
TitleOxidized and reduced structures of a mutant Plastocyanin of fern
ComponentsPLASTOCYANIN
KeywordsELECTRON TRANSPORT / FERN / METAL-BINDING / THYLAKOID / TRANSPORT
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
Similarity search - Component
Biological speciesDRYOPTERIS CRASSIRHIZOMA (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHulsker, R. / Thomassen, E.A.J. / Ubbink, M.
Citation
Journal: J.Am.Chem.Soc. / Year: 2007
Title: Protonation of a Histidine Copper Ligand in Fern Plastocyanin.
Authors: Hulsker, R. / Mery, A. / Thomassen, E.A.J. / Ranieri, A. / Sola, M. / Verbeet, M.P. / Kohzuma, T. / Ubbink, M.
#1: Journal: Biochemistry / Year: 1999
Title: Structure Comparison between Oxidized and Reduced Plastocyanin from a Fer, Dryopteris Crassirhizoma
Authors: Inoue, T. / Gotowda, M. / Sugawara, H. / Kohzuma, T. / Yoshizaki, F. / Sugimura, Y. / Kai, Y.
History
DepositionAug 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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 / 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 / _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_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: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8902
Polymers10,8261
Non-polymers641
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.921, 72.921, 29.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PLASTOCYANIN


Mass: 10826.036 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: OXIDIZED FORM / Source: (gene. exp.) DRYOPTERIS CRASSIRHIZOMA (plant) / Plasmid: PETG36P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIB8
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 36 TO PRO PARTICIPATES IN ELECTRON TRANSFER BETWEEN THE ...ENGINEERED RESIDUE IN CHAIN A, GLY 36 TO PRO PARTICIPATES IN ELECTRON TRANSFER BETWEEN THE CYTOCHROME B6-F COMPLEX AND P700 IN PHOTOSYSTEM I.

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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: 2.1 Å3/Da / Density % sol: 40.1 %
Crystal growpH: 4.5 / Details: 2.6 M AMMONIUM SULPHATE 0.1M SODIUM ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372
DetectorType: MARRESEARCH / Detector: CCD / Date: May 6, 2005 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.76→21.57 Å / Num. obs: 9095 / % possible obs: 99.8 % / Redundancy: 10.89 % / Biso Wilson estimate: 20.07 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.91
Reflection shellResolution: 1.76→1.78 Å / Redundancy: 10.89 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9.48 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KDJ

1kdj


Resolution: 1.76→63.12 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.927 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED LOOP AA68-AA70
RfactorNum. reflection% reflectionSelection details
Rfree0.24 428 4.7 %RANDOM
Rwork0.191 ---
obs0.193 8652 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.81 Å2
Baniso -1Baniso -2Baniso -3
1--3.41 Å2-1.71 Å20 Å2
2---3.41 Å20 Å2
3---5.12 Å2
Refinement stepCycle: LAST / Resolution: 1.76→63.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 1 87 849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9721059
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99526.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93915122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02590
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2337
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2538
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9871.5519
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3942825
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.213285
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2544.5234
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.259 31
Rwork0.234 637
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.3026-2.125-0.11022.85930.24440.9867-0.00850.093-0.1140.0266-0.05320.2474-0.01470.12210.0617-0.08010.0052-0.0044-0.0465-0.0065-0.022221.4879-8.9313-0.092
212.8386-3.0616-0.76315.0942-0.0291.1625-0.03430.11120.5473-0.02890.0935-0.18080.05610.0937-0.0592-0.0823-0.0082-0.02-0.0380.002-0.136526.8072-6.5983-0.0499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION2A51 - 102

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