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- PDB-1jxg: The 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastoc... -

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Basic information

Entry
Database: PDB / ID: 1jxg
TitleThe 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastocyanin Bearing a 21-25 Engeneered Disulfide Bridge
ComponentsPLASTOCYANIN A
KeywordsPHOTOSYNTHESIS / BETA BARREL
Function / homology
Function and homology information


: / chloroplast thylakoid lumen / chloroplast thylakoid membrane / 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 (I) ION / Plastocyanin A, chloroplastic
Similarity search - Component
Biological speciesPopulus nigra (black poplar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMilani, M. / Andolfi, L. / Cannistraro, S. / Verbeet, M.P. / Bolognesi, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The 1.6 A resolution crystal structure of a mutant plastocyanin bearing a 21-25 engineered disulfide bridge.
Authors: Milani, M. / Andolfi, L. / Cannistraro, S. / Verbeet, M.P. / Bolognesi, M.
History
DepositionSep 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 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 A
B: PLASTOCYANIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4015
Polymers21,1782
Non-polymers2233
Water4,972276
1
A: PLASTOCYANIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6522
Polymers10,5891
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PLASTOCYANIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7483
Polymers10,5891
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.381, 49.306, 76.576
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 PLASTOCYANIN A


Mass: 10588.816 Da / Num. of mol.: 2 / Mutation: I21C, E25C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus nigra (black poplar) / Variant: ITALICA / Production host: Escherichia coli (E. coli) / References: UniProt: P00299
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.5 Mammonium sulfate1reservoir
20.05 Mpotassium phosphate1reservoirpH7.0
38.8 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 29, 2000
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. all: 25069 / Num. obs: 24587 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 4 / Num. unique all: 862 / % possible all: 71.6
Reflection
*PLUS
Lowest resolution: 35 Å / Num. obs: 25069 / Num. measured all: 135535
Reflection shell
*PLUS
% possible obs: 71.6 % / Mean I/σ(I) obs: 4.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PLC

1plc


Resolution: 1.6→41 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 1235 5.1 %RANDOM
Rwork0.14464 ---
all0.14782 22927 --
obs0.14782 22927 99.3 %-
Displacement parametersBiso mean: 19.615 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.26 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 7 280 1779
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.3371
X-RAY DIFFRACTIONp_mcangle_it4.822
X-RAY DIFFRACTIONp_scbond_it6.4413
X-RAY DIFFRACTIONp_scangle_it7.6853
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.45

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