SAXSdb — 2jxm

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

Plastocyanin

Prochlorothrix hollandica

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 35–131	Not recorded	Cytochrome f × 1 （Q8RN59） CU COPPER (II) ION × 1 HEC HEME C × 1	SOLUTION NMR NMR measurement conditions：pH 6；300 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition：85 uM [U-99% 15N] plastocyanin, 50 uM cytochrome f, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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 2JXM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B3I NMR SOLUTION STRUCTURE OF PLASTOCYANIN FROM THE PHOTOSYNTHETIC PROKARYOTE, PROCHLOROTHRIX HOLLANDICA (MINIMIZED AVERAGE STRUCTURE) Deposited 1998-12-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–131（97 aa）	Mutation：T2S	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 20mM POTASSIUM PHOSPHATE；Pressure 1 NMR sample composition 90% WATER/10% D2O	Resolution not provided
2B3I NMR SOLUTION STRUCTURE OF PLASTOCYANIN FROM THE PHOTOSYNTHETIC PROKARYOTE, PROCHLOROTHRIX HOLLANDICA (19 STRUCTURES) Deposited 1998-12-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–131（97 aa）	Mutation：T2S	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 20mM POTASSIUM PHOSPHATE；Pressure 1 NMR sample composition 90% WATER/10% D2O	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLAS_PROHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 35–131

Cytochrome f

Prochlorothrix hollandica

UniProt Q8RN59

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 47–295	Not recorded	Plastocyanin × 1 （P50057） CU COPPER (II) ION × 1 HEC HEME C × 1	SOLUTION NMR NMR measurement conditions：pH 6；300 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition：85 uM [U-99% 15N] plastocyanin, 50 uM cytochrome f, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q8RN59_PROHO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–249； UniProt 47–295

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	2jxm
Deposition date deposition_date	2007-11-22
Structure title title	Ensemble of twenty structures of the Prochlorothrix hollandica plastocyanin- cytochrome f complex
Keywords keywords	Copper, Electron transport, Metal-binding, Transport; ELECTRON TRANSPORT
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	23.45 Å
Radius of gyration Rg (electron density) rg_electron	23.42 Å
Forward intensity I(0) i0	7399150000.00
Molecular weight molecular_weight	747930.0 kDa
Excluded volume excluded_volume	938790 Å³
Envelope volume envelope_volume	76240 Å³
Hydration-shell volume shell_volume	26537 Å³
Envelope diameter envelope_diameter	86.8 Å
Shell Rg shell_rg	31.54 Å
Envelope Rg envelope_rg	25.17 Å
Shape Rg shape_rg	23.42 Å
Total Rg total_rg	23.49 Å
Total atoms total_atoms	103580
Residues n_residues	6920
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	80.4 Å
Rg (real space) rg_real	23.57 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	7.3990e+09
I(0) uncertainty (real space) i0_real_error	1.0530e+08
Rg (reciprocal space) rg_reciprocal	23.54 Å
I(0) (reciprocal space) i0_reciprocal	7399000000.0000
Solution quality estimate total_estimate	0.8693
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.471
Kurtosis Kurtosis kurtosis	-0.249
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4271000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.864; Smooth: 0.973

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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
Molecular weight formula_weight	10148.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	103580

ASVQIKMGTDKYAPLYEPKALSISAGDTVEFVMNKVGPHNVIFDKVPAGESAPALSNTKLAIAPGSFYSVTLGTPGTYSFYCTPHRGAGMVGTITVE

来源 Source

来源生物 organism	Prochlorothrix hollandica
NCBI Class编号 ncbi_taxonomy_id	1223
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cytochrome f
Molecular weight formula_weight	26611.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

YPFYAQYNYDSPREATGKIVCANCHLAKKTVEIEVPQAVLPDTVFKAVVKVPYDLDIQQVQADGSPSGLNVGAVLMLPEGFKLAPPERVDEELMEEVGDFYYLVTPYSETDENILLAGPLPGEDYQEMIFPILSPNPATDAGVYFGKYSIHLGGNRGRGQVYPTGELSNNNAFSASIAGTIAAIEDNGFGFDVTIQPEDGDAVVTSILPGPELIVAVGDTVEAGQLLTTNPNVGGFGQMDSEIVLQSSS

来源 Source

来源生物 organism	Prochlorothrix hollandica
NCBI Class编号 ncbi_taxonomy_id	1223
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2jxma_
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	d2jxmb1
Class class	i — Low resolution protein structures
Fold Fold fold	i.4 — Electron transport chains
Superfamily Superfamily superfamily	i.4.1 — Electron transport chains
Family Family family	i.4.1.1 — Electron transport chains

CATH v4.4 (3 domains)

Domain ID domain_id	2jxmA00
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	2jxmB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	830 — Cytochrome f large domain

Domain ID domain_id	2jxmB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

fit	/app/data/saxs_computation/jx/2jxm/2jxm.fit
pddf	/app/data/pr_computation/jx/2jxm/2jxm.pr.out
profile	/app/data/saxs_computation/jx/2jxm/2jxm.dat

Ensemble of twenty structures of the Prochlorothrix hollandica plastocyanin- cytochrome f complex

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

Plastocyanin

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome f

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)