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- PDB-1pnd: ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: TWO... -

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Basic information

Entry
Database: PDB / ID: 1pnd
TitleACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: TWO INDEPENDENT REFINEMENTS OF THE STRUCTURE OF POPLAR PLASTOCYANIN AT 173K
ComponentsPLASTOCYANIN
KeywordsELECTRON TRANSPORT
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 (II) ION / Plastocyanin A, chloroplastic
Similarity search - Component
Biological speciesPopulus nigra (black poplar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsFields, B.A. / Guss, J.M. / Freeman, H.C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K.
Authors: Fields, B.A. / Bartsch, H.H. / Bartunik, H.D. / Cordes, F. / Guss, J.M. / Freeman, H.C.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Accuracy and Precision in Protein Structure Analysis: Restrained Least-Squares Refinement of the Structure of Poplar Plastocyanin at 1.33 Angstroms Resolution
Authors: Guss, J.M. / Bartunik, H.D. / Freeman, H.C.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Oxidised Poplar Plastocyanin at 1.6 Angstroms Resolution
Authors: Guss, J.M. / Freeman, H.C.
#3: Journal: Nature / Year: 1978
Title: X-Ray Crystal Structure Analysis of Plastocyanin at 2.7 Angstroms Resolution
Authors: Colman, P.M. / Freeman, H.C. / Guss, J.M. / Murata, M. / Norris, V.A. / Ramshaw, J.A.M. / Venkatappa, M.P. / Freeman, H.C.
#4: Journal: J.Mol.Biol. / Year: 1977
Title: Preliminary Crystallographic Data for a Copper Containing Protein, Plastocyanin
Authors: Chapman, G.V. / Colman, P.M. / Freeman, H.C. / Guss, J.M. / Murata, M. / Norris, V.A. / Ramashaw, J.A.M. / Venkatappa, M.P. / Freeman, H.C.
History
DepositionSep 22, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 8, 2012Group: Derived calculations
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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_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)10,5572
Polymers10,4941
Non-polymers641
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.180, 46.290, 56.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 16 / 2: CIS PROLINE - PRO 36
3: THE LIGANDS OF THE CU ATOM ARE ND1 HIS 37, SG CYS 84, ND1 HIS 87, AND SD MET 92.

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Components

#1: Protein PLASTOCYANIN


Mass: 10493.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus nigra (black poplar) / References: UniProt: P00299
#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.: 171 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.48 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Details: taken from Chapman, G.V. et al (1977). J. Mol. Biol., 110, 187-189.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
20.1 Msodium phosphate1reservoir
32.6 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31
DetectorType: ENRAF-NONIUS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
EREFrefinement
PROLSQrefinement
RefinementResolution: 1.6→6 Å
Details: THE STRUCTURE WAS REFINED INDEPENDENTLY IN SYDNEY USING PROLSQ AND IN HAMBURG USING EREF. THE STRUCTURES WERE COMPARED ONLY AFTER THE REFINEMENTS WERE COMPLETE.
RfactorNum. reflection% reflection
Rwork0.153 --
obs-7393 69.3 %
Refinement stepCycle: LAST / Resolution: 1.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms738 0 1 171 910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.153
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.011
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 6 Å / Num. reflection obs: 7393 / Rfactor obs: 0.135
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11 Å2

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