SAXSdb — 1jxg

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PLASTOCYANIN A

Populus nigra

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 70–168	Mutation：I21C, E25C	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.205
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 70–168	Mutation：I21C, E25C	CU1 COPPER (I) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.205

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1JXG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PLC ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF POPLAR PLASTOCYANIN AT 1.33 ANGSTROMS RESOLUTION Deposited 1992-03-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.33 Å
1PNC ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: TWO INDEPENDENT REFINEMENTS OF THE STRUCTURE OF POPLAR PLASTOCYANIN AT 173K Deposited 1993-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
1PND ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: TWO INDEPENDENT REFINEMENTS OF THE STRUCTURE OF POPLAR PLASTOCYANIN AT 173K Deposited 1993-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
1TKW The transient complex of poplar plastocyanin with turnip cytochrome f determined with paramagnetic NMR Deposited 2004-06-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1 HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1 NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 11 mM；Pressure 1 NMR sample composition 0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in oxidized state in 10 mM sodium phosphate pH 6.0 \| 94% H2O, 6% D2O NMR sample composition 0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in reduced state in 10 mM sodium phosphate pH 6.0 + 1 mM sodium ascorbate \| 94% H2O, 6% D2O	Resolution not provided
2PCY THE CRYSTAL STRUCTURE OF POPLAR APOPLASTOCYANIN AT 1.8-ANGSTROMS RESOLUTION. THE GEOMETRY OF THE COPPER-BINDING SITE IS CREATED BY THE POLYPEPTIDE Deposited 1983-11-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
3PCY THE CRYSTAL STRUCTURE OF MERCURY-SUBSTITUTED POPLAR PLASTOCYANIN AT 1.9-ANGSTROMS RESOLUTION Deposited 1985-12-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
4DP7 The 1.08 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 4.0 Deposited 2012-02-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.08 Å R-free 0.142
4DP8 The 1.07 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 4.0 Deposited 2012-02-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU1 COPPER (I) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.07 Å R-free 0.165
4DP9 The 1.00 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 6.0 Deposited 2012-02-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.00 Å R-free 0.144
4DPA The 1.05 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 6.0 Deposited 2012-02-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.05 Å R-free 0.155
4DPB The 1.00 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 8.0 Deposited 2012-02-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.00 Å R-free 0.136
4DPC The 1.06 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 8.0 Deposited 2012-02-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.06 Å R-free 0.155
4PCY CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES Deposited 1986-09-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å
5PCY CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES Deposited 1986-09-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
6PCY CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES Deposited 1986-09-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLAS1_POPNI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–100； UniProt 70–168 Author chain B； PDBConstruct 2–100； UniProt 70–168

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1jxg
Deposition date deposition_date	2001-09-07
Structure title title	The 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastocyanin Bearing a 21-25 Engeneered Disulfide Bridge
Keywords keywords	BETA BARREL, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.80 Å
Radius of gyration Rg (electron density) rg_electron	19.97 Å
Forward intensity I(0) i0	8662320.00
Molecular weight molecular_weight	21369.0 kDa
Excluded volume excluded_volume	26340 Å³
Envelope volume envelope_volume	32259 Å³
Hydration-shell volume shell_volume	13889 Å³
Envelope diameter envelope_diameter	67.7 Å
Shell Rg shell_rg	25.24 Å
Envelope Rg envelope_rg	19.67 Å
Shape Rg shape_rg	19.96 Å
Total Rg total_rg	20.72 Å
Total atoms total_atoms	1489
Residues n_residues	200
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.5 Å
Rg (real space) rg_real	20.81 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	8.6620e+06
I(0) uncertainty (real space) i0_real_error	9.7010e+04
Rg (reciprocal space) rg_reciprocal	20.81 Å
I(0) (reciprocal space) i0_reciprocal	8662000.0000
Solution quality estimate total_estimate	0.9029
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.0 Å
Skewness Skewness skewness	0.199
Kurtosis Kurtosis kurtosis	-0.744
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1084000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PLASTOCYANIN A
Molecular weight formula_weight	10588.8 kDa
Mutation mutation	I21C, E25C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1781

MIDVLLGADDGSLAFVPSEFSCSPGCKIVFKNNAGFPHNIVFDEDSIPSGVDASKISMSEEDLLNAKGETFEVALSNKGEYSFYCSPHQGAGMVGKVTVN

来源 Source

来源生物 organism	Populus nigra
NCBI Class编号 ncbi_taxonomy_id	3691
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (I) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	276

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1jxga_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d1jxgb_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

CATH v4.4 (2 domains)

Domain ID domain_id	1jxgA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1jxgB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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8. Citations (1)

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Unit-cell length a length_a	47.381 Å
Unit-cell length b length_b	49.306 Å
Unit-cell length c length_c	76.576 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	41.000 Å
R factor r_factor	0.1478
R_work r_work	0.1446
R_free r_free	0.2053

fit	/app/data/saxs_computation/jx/1jxg/1jxg.fit
pddf	/app/data/pr_computation/jx/1jxg/1jxg.pr.out
profile	/app/data/saxs_computation/jx/1jxg/1jxg.dat

The 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastocyanin Bearing a 21-25 Engeneered Disulfide Bridge

1. Protein Identity and Related Structures Protein Identity & Related Structures

PLASTOCYANIN A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction