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- PDB-2w88: Plastocyanin variant with N-terminal Methionine - open structure -

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Open data


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Basic information

Entry
Database: PDB / ID: 2w88
TitlePlastocyanin variant with N-terminal Methionine - open structure
ComponentsPLASTOCYANIN
KeywordsELECTRON TRANSPORT / PROTEIN INTERACTIONS / TRANSPORT / CUPREDOXIN / SELF-ASSEMBLY / METAL-BINDING
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / electron transfer activity / copper ion binding
Similarity search - Function
Plastocyanin, cyanobacteria / 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 ...Plastocyanin, cyanobacteria / 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 speciesPHORMIDIUM LAMINOSUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsCrowley, P.B. / Matias, P.M. / Khan, A.R.
CitationJournal: Chemistry / Year: 2009
Title: Metal-Mediated Self-Assembly of a Beta-Sandwich Protein.
Authors: Crowley, P.B. / Matias, P.M. / Khan, A.R. / Roessle, M. / Svergun, D.I.
History
DepositionJan 14, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
B: PLASTOCYANIN
C: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,33713
Polymers34,6893
Non-polymers64910
Water00
1
A: PLASTOCYANIN
B: PLASTOCYANIN
C: PLASTOCYANIN
hetero molecules

A: PLASTOCYANIN
B: PLASTOCYANIN
C: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,67526
Polymers69,3786
Non-polymers1,29720
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area6320 Å2
ΔGint-12.5 kcal/mol
Surface area33730 Å2
MethodPQS
Unit cell
Length a, b, c (Å)127.700, 127.700, 94.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 0 - 105 / Label seq-ID: 1 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(0.79062, 0.29652, 0.53572), (-0.34904, -0.5006, 0.7922), (0.50308, -0.81331, -0.29229)-17.38811, 32.12272, 44.8758
2given(0.79397, -0.31975, 0.51708), (0.31946, -0.50421, -0.80232), (0.51726, 0.80221, -0.29818)1.46014, 58.18138, -3.57527

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Components

#1: Protein PLASTOCYANIN


Mass: 11562.996 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHORMIDIUM LAMINOSUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q51883
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
Sequence detailsNO SIGNAL PEPTIDE PRESENT AND N-TERMINAL INSERTION OF MET0

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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: 6.45 Å3/Da / Density % sol: 81 % / Description: NONE
Crystal growDetails: 0.1 M ZINC ACETATE, 0.4 M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGING PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.89→47.78 Å / Num. obs: 19857 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 54.38 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.3
Reflection shellResolution: 2.89→3.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0063refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CVB

3cvb


Resolution: 2.89→110.43 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.904 / SU B: 18.96 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUALS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22285 1012 5.1 %RANDOM
Rwork0.19433 ---
obs0.19578 18824 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.099 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.89→110.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 10 0 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222539
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9583408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59225.143105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11815393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.273153
X-RAY DIFFRACTIONr_chiral_restr0.0870.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211935
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4041.51586
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77122559
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4463953
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2044.5849
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A424medium positional0.110.5
2B424medium positional0.140.5
3C424medium positional0.110.5
1A389loose positional0.255
2B389loose positional0.375
3C389loose positional0.245
1A424medium thermal1.22
2B424medium thermal1.222
3C424medium thermal0.872
1A389loose thermal1.3310
2B389loose thermal1.4810
3C389loose thermal1.1110
LS refinement shellResolution: 2.894→2.969 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 58
Rwork0.302 1356
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)
12.8942-0.09770.28723.12460.73711.55540.05820.2423-0.094-0.2023-0.0483-0.02090.0786-0.0485-0.00990.08110.0112-0.01450.037-0.01820.0125-12.037822.2092-3.3336
22.2347-0.1761-0.91961.8816-0.57672.9314-0.0013-0.2372-0.16420.14630.0310.25730.0518-0.1447-0.02970.0509-0.0059-0.0030.05090.02110.066-22.084522.598721.7165
31.79750.00670.17193.918-1.87222.46030.02570.1250.2456-0.066-0.06930.0835-0.2426-0.07080.04360.09850.0207-0.030.01930.01180.0483-16.926645.76889.038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 105
2X-RAY DIFFRACTION2B0 - 105
3X-RAY DIFFRACTION3C0 - 105

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