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- PDB-2w8c: Plastocyanin variant with N-terminal Methionine - closed structure -

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Basic information

Entry
Database: PDB / ID: 2w8c
TitlePlastocyanin variant with N-terminal Methionine - closed 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: 1.8 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 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Nov 20, 2013Group: Data collection / Derived calculations
Revision 1.4Dec 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5158
Polymers23,1262
Non-polymers3896
Water2,882160
1
A: PLASTOCYANIN
hetero molecules

A: PLASTOCYANIN
hetero molecules

A: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,27212
Polymers34,6893
Non-polymers5839
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area2760 Å2
ΔGint-205.4 kcal/mol
Surface area14580 Å2
MethodPISA
2
B: PLASTOCYANIN
hetero molecules

B: PLASTOCYANIN
hetero molecules

B: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,27212
Polymers34,6893
Non-polymers5839
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area2810 Å2
ΔGint-148.4 kcal/mol
Surface area14470 Å2
MethodPISA
3
A: PLASTOCYANIN
hetero molecules

A: PLASTOCYANIN
hetero molecules

A: PLASTOCYANIN
hetero molecules

B: PLASTOCYANIN
hetero molecules

B: PLASTOCYANIN
hetero molecules

B: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,54424
Polymers69,3786
Non-polymers1,16618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation4_455x-1/3,y+1/3,z+1/31
crystal symmetry operation5_445-y-1/3,x-y-2/3,z+1/31
crystal symmetry operation6_555-x+y+2/3,-x+1/3,z+1/31
Buried area6890 Å2
ΔGint-369.8 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.740, 55.740, 197.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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

NCS oper: (Code: given
Matrix: (-0.99189, 0.12694, 0.00654), (0.12706, 0.99157, 0.02524), (-0.00328, 0.02587, -0.99966)
Vector: 29.6915, 12.11097, 52.52563)

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Components

#1: Protein PLASTOCYANIN


Mass: 11562.996 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNO SIGNAL PEPTIDE PRESENT AND N-TERMINAL MET INSERTION

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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: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 5% PEG 8K, 0.1M ZINC ACETATE, 0.2 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 IMAGE PLATE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→46.9 Å / Num. obs: 20932 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 17.71 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.7 / % possible all: 93.7

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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 2W88 CHAIN A

2w88


Resolution: 1.8→65.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.764 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUALS ONLY. RESIDUES VAL 32 A, MET 65 A, SER 78 A, ARG 93 A, MET 65 B AND ARG 93 B WERE MODELLED WITH TWO ALTERNATIVE SIDE-CHAIN CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1072 5.1 %RANDOM
Rwork0.173 ---
obs0.176 19859 99.1 %-
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: 20.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20.63 Å20 Å2
2--1.27 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 6 160 1792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221730
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.962332
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37424.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53115276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.64154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211324
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_it1.7554500
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.636815
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.614312
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1666280
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
1A420medium positional0.260.5
2B420medium positional0.260.5
1A390loose positional0.565
2B390loose positional0.565
1A420medium thermal3.285
2B420medium thermal3.285
1A390loose thermal4.4910
2B390loose thermal4.4910
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 54
Rwork0.348 1315
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)
11.4388-0.69550.43751.1536-0.43582.7728-0.0551-0.12780.0001-0.02310.1182-0.0552-0.19870.1758-0.06310.0201-0.01550.00750.0371-0.0160.026613.66157.063540.8287
22.0021-0.14440.14420.74010.21472.5776-0.0460.0852-0.06020.0770.0824-0.0291-0.1613-0.0886-0.03640.02180.01590.00160.0206-0.00180.027315.3164-7.312311.3994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 105
2X-RAY DIFFRACTION2B0 - 105

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