SAXSdb — 1cfz

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

HYDROGENASE 2 MATURATION PROTEASE

Escherichia coli

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 1–162	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.20 Å R-free 0.259
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–162	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.20 Å R-free 0.259
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–162	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.20 Å R-free 0.259
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–162	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.20 Å R-free 0.259
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–162	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.20 Å R-free 0.259
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–162	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.20 Å R-free 0.259

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	HYBD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 1–162 Author chain B； PDBConstruct 1–162； UniProt 1–162 Author chain C； PDBConstruct 1–162； UniProt 1–162 Author chain D； PDBConstruct 1–162； UniProt 1–162 Author chain E； PDBConstruct 1–162； UniProt 1–162 Author chain F； PDBConstruct 1–162； UniProt 1–162

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	1cfz
Deposition date deposition_date	1999-03-23
Structure title title	HYDROGENASE MATURATING ENDOPEPTIDASE HYBD FROM E. COLI
Keywords keywords	HYDROGENASE, MATURATION, METZINCINS, NICKEL, PROTEASE; HYDROGENASE
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	37.86 Å
Radius of gyration Rg (electron density) rg_electron	37.46 Å
Forward intensity I(0) i0	161789000.00
Molecular weight molecular_weight	105450.0 kDa
Excluded volume excluded_volume	133360 Å³
Envelope volume envelope_volume	178610 Å³
Hydration-shell volume shell_volume	40865 Å³
Envelope diameter envelope_diameter	125.4 Å
Shell Rg shell_rg	42.24 Å
Envelope Rg envelope_rg	36.42 Å
Shape Rg shape_rg	37.48 Å
Total Rg total_rg	37.75 Å
Total atoms total_atoms	7356
Residues n_residues	972
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	122.1 Å
Rg (real space) rg_real	37.78 Å
Rg uncertainty (real space) rg_real_error	1.16 Å
I(0) (real space) i0_real	1.6180e+08
I(0) uncertainty (real space) i0_real_error	2.8760e+06
Rg (reciprocal space) rg_reciprocal	37.83 Å
I(0) (reciprocal space) i0_reciprocal	161800000.0000
Solution quality estimate total_estimate	0.8309
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.5 Å
Skewness Skewness skewness	0.157
Kurtosis Kurtosis kurtosis	-0.608
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9131000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HYDROGENASE 2 MATURATION PROTEASE
Molecular weight formula_weight	17490.3 kDa
EC 编号 ec_number	3.4.-.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7630

MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRSDS

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	274

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1cfza_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.1 — HybD-like
Family Family family	c.56.1.1 — Hydrogenase maturating endopeptidase HybD

Domain ID domain_id	d1cfzb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.1 — HybD-like
Family Family family	c.56.1.1 — Hydrogenase maturating endopeptidase HybD

Domain ID domain_id	d1cfzc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.1 — HybD-like
Family Family family	c.56.1.1 — Hydrogenase maturating endopeptidase HybD

Domain ID domain_id	d1cfzd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.1 — HybD-like
Family Family family	c.56.1.1 — Hydrogenase maturating endopeptidase HybD

Domain ID domain_id	d1cfze_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.1 — HybD-like
Family Family family	c.56.1.1 — Hydrogenase maturating endopeptidase HybD

Domain ID domain_id	d1cfzf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.1 — HybD-like
Family Family family	c.56.1.1 — Hydrogenase maturating endopeptidase HybD

CATH v4.4 (6 domains)

Domain ID domain_id	1cfzA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1450 — HybD-like

Domain ID domain_id	1cfzB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1450 — HybD-like

Domain ID domain_id	1cfzC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1450 — HybD-like

Domain ID domain_id	1cfzD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1450 — HybD-like

Domain ID domain_id	1cfzE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1450 — HybD-like

Domain ID domain_id	1cfzF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1450 — HybD-like

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8. Citations (1)

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Unit-cell length a length_a	128.000 Å
Unit-cell length b length_b	128.000 Å
Unit-cell length c length_c	139.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 32 1 2
Space-group number int_tables_number	153
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2240
R_free r_free	0.2590

fit	/app/data/saxs_computation/cf/1cfz/1cfz.fit
pddf	/app/data/pr_computation/cf/1cfz/1cfz.pr.out
profile	/app/data/saxs_computation/cf/1cfz/1cfz.dat

HYDROGENASE MATURATING ENDOPEPTIDASE HYBD FROM E. COLI

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

HYDROGENASE 2 MATURATION PROTEASE

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