SAXSdb — 1a4c

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

AZURIN

Achromobacter denitrificans

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 21–149 Chain C； UniProt 21–149	Mutation：M121H	CU COPPER (II) ION × 2 SO4 SULFATE ION × 2 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.45 Å
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 21–149 Chain D； UniProt 21–149	Mutation：M121H	CU COPPER (II) ION × 2 SO4 SULFATE ION × 2 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.45 Å

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 1A4C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A4A AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, DATA COLLECTED AT 16 DEGREES CELSIUS Deposited 1998-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–149（129 aa）	Mutation：M121H	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.89 Å
1A4A AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, DATA COLLECTED AT 16 DEGREES CELSIUS Deposited 1998-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–149（129 aa）	Mutation：M121H	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.89 Å
1A4B AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, DATA COLLECTED AT-180 DEGREES CELSIUS Deposited 1998-01-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–149（129 aa） Chain B 21–149（129 aa）	Mutation：M121H Mutation：M121H	CU COPPER (II) ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.91 Å
1AIZ STRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANGSTROMS RESOLUTION Deposited 1993-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–149（129 aa） Chain B 21–149（129 aa）	Not recorded	CD CADMIUM ION × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1AZB STRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANGSTROMS RESOLUTION Deposited 1992-12-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–149（129 aa） Chain B 21–149（129 aa）	Not recorded	CU COPPER (II) ION × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1AZC STRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANGSTROMS RESOLUTION Deposited 1992-12-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–149（129 aa） Chain B 21–149（129 aa）	Not recorded	CU COPPER (II) ION × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1URI AZURIN MUTANT WITH MET 121 REPLACED BY GLN Deposited 1996-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–149（129 aa）	Mutation：M121Q	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.94 Å
1URI AZURIN MUTANT WITH MET 121 REPLACED BY GLN Deposited 1996-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–149（129 aa）	Mutation：M121Q	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.94 Å
2AZA STRUCTURE OF AZURIN FROM ALCALIGENES DENITRIFICANS. REFINEMENT AT 1.8 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES Deposited 1986-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–149（129 aa）	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
2AZA STRUCTURE OF AZURIN FROM ALCALIGENES DENITRIFICANS. REFINEMENT AT 1.8 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES Deposited 1986-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–149（129 aa）	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AZUR_ALCDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–129； UniProt 21–149 Author chain B； PDBConstruct 1–129； UniProt 21–149 Author chain C； PDBConstruct 1–129； UniProt 21–149 Author chain D； PDBConstruct 1–129； UniProt 21–149

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	1a4c
Deposition date deposition_date	1998-01-28
Structure title title	AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 3.5 CRYSTAL FORM, DATA COLLECTED AT-180 DEGREES CELSIUS
Keywords keywords	ELECTRON TRANSPORT, CUPROPROTEIN; ELECTRON TRANSPORT
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	42.25 Å
Radius of gyration Rg (electron density) rg_electron	42.55 Å
Forward intensity I(0) i0	53840600.00
Molecular weight molecular_weight	56694.0 kDa
Excluded volume excluded_volume	69626 Å³
Envelope volume envelope_volume	107920 Å³
Hydration-shell volume shell_volume	21918 Å³
Envelope diameter envelope_diameter	133.3 Å
Shell Rg shell_rg	46.51 Å
Envelope Rg envelope_rg	40.15 Å
Shape Rg shape_rg	42.54 Å
Total Rg total_rg	42.80 Å
Total atoms total_atoms	4830
Residues n_residues	516
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	129.9 Å
Rg (real space) rg_real	42.54 Å
Rg uncertainty (real space) rg_real_error	1.46 Å
I(0) (real space) i0_real	5.3840e+07
I(0) uncertainty (real space) i0_real_error	9.7960e+05
Rg (reciprocal space) rg_reciprocal	42.26 Å
I(0) (reciprocal space) i0_reciprocal	53820000.0000
Solution quality estimate total_estimate	0.6403
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.195
Kurtosis Kurtosis kurtosis	-0.900
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	981600.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.317; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.368; Smooth: 0.003

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	AZURIN
Molecular weight formula_weight	14004.9 kDa
Mutation mutation	M121H
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6192

AQCEATIESNDAMQYDLKEMVVDKSCKQFTVHLKHVGKMAKSAMGHNWVLTKEADKEGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMHKGTLKLSN

来源 Source

来源生物 organism	Achromobacter denitrificans
NCBI Class编号 ncbi_taxonomy_id	32002
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

Entity 4 Entity 4 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	454

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a4ca_
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	d1a4cb_
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	d1a4cc_
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	d1a4cd_
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 (4 domains)

Domain ID domain_id	1a4cA00
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	1a4cB00
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	1a4cC00
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	1a4cD00
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	99.600 Å
Unit-cell length b length_b	100.010 Å
Unit-cell length c length_c	53.940 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2093
R_work r_work	0.2093
R_free r_free	—

fit	/app/data/saxs_computation/a4/1a4c/1a4c.fit
pddf	/app/data/pr_computation/a4/1a4c/1a4c.pr.out
profile	/app/data/saxs_computation/a4/1a4c/1a4c.dat

AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 3.5 CRYSTAL FORM, DATA COLLECTED AT-180 DEGREES CELSIUS

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

AZURIN

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