SAXSdb — 1bwz

▼

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

PROTEIN (DIAMINOPIMELATE EPIMERASE)

Haemophilus influenzae

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 1–274	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.72 Å R-free 0.242

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 1BWZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GQZ Refinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A Deposited 2001-12-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–274（274 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M IMIDIZOLE PH 6.5,	Resolution 1.75 Å R-free 0.196
2GKE Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor LL-AziDAP Deposited 2006-04-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–274（274 aa）	Not recorded	ZDP (2S,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 GOL GLYCEROL × 1 ACY ACETIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.8 M sodium acetate and 0.1 M HEPES (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.35 Å R-free 0.168
2GKJ Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor DL-AZIDAP Deposited 2006-04-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–274（274 aa）	Not recorded	ZDR (2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID × 1 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.8 M sodium acetate and 0.1 M HEPES (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.210
2Q9H Crystal structure of the C73S mutant of diaminopimelate epimerase Deposited 2007-06-12	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 1–274（274 aa）	Mutation：C73S	TLA L(+)-TARTARIC ACID × 1 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.8 M potassium sodium tartrate tetrahydrate, 0.2 M NaCl, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.240
2Q9J Crystal structure of the C217S mutant of diaminopimelate epimerase Deposited 2007-06-12	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 1–274（274 aa）	Mutation：C217S Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；(0.8 M potassium sodium tartrate tetrahydrate, 0.2 M NaCl, 0.1M HEPES), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.253

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DAPF_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–274； UniProt 1–274

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bwz
Deposition date deposition_date	1998-09-29
Structure title title	DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE
Keywords keywords	METABOLIC ROLE, STRUCTURAL CLASSIFICATION, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.84 Å
Radius of gyration Rg (electron density) rg_electron	19.07 Å
Forward intensity I(0) i0	16584000.00
Molecular weight molecular_weight	30184.0 kDa
Excluded volume excluded_volume	37535 Å³
Envelope volume envelope_volume	43815 Å³
Hydration-shell volume shell_volume	19268 Å³
Envelope diameter envelope_diameter	65.5 Å
Shell Rg shell_rg	25.16 Å
Envelope Rg envelope_rg	19.32 Å
Shape Rg shape_rg	19.09 Å
Total Rg total_rg	19.84 Å
Total atoms total_atoms	2117
Residues n_residues	274
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

▼

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

Maximum dimension Dmax dmax	64.0 Å
Rg (real space) rg_real	19.76 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	1.6580e+07
I(0) uncertainty (real space) i0_real_error	1.9730e+05
Rg (reciprocal space) rg_reciprocal	19.77 Å
I(0) (reciprocal space) i0_reciprocal	16580000.0000
Solution quality estimate total_estimate	0.7109
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.268
Kurtosis Kurtosis kurtosis	-0.399
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5865000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 0.210; Positv: 1.000; Valcen: 0.999; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bwza1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

Domain ID domain_id	d1bwza2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.1 — Diaminopimelate epimerase

CATH v4.4 (2 domains)

Domain ID domain_id	1bwzA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	1bwzA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

▶

8. Citations (1)

▶

Unit-cell length a length_a	102.100 Å
Unit-cell length b length_b	115.400 Å
Unit-cell length c length_c	66.300 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.720 Å
Low-resolution limit resolution_low	23.790 Å
R factor r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2420

Description description	PROTEIN (DIAMINOPIMELATE EPIMERASE)
Molecular weight formula_weight	30295.6 kDa
EC 编号 ec_number	5.1.1.7
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2146

DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE

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

PROTEIN (DIAMINOPIMELATE EPIMERASE)

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Haemophilus influenzae
NCBI Class编号 ncbi_taxonomy_id	727
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

fit	/app/data/saxs_computation/bw/1bwz/1bwz.fit
pddf	/app/data/pr_computation/bw/1bwz/1bwz.pr.out
profile	/app/data/saxs_computation/bw/1bwz/1bwz.dat