SAXSdb — 5d7w

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

Serralysin

Serratia marcescens

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 20–487	Fragment：UNP residues 20-487 Mutation：P250L	ZN ZINC ION × 1 CA CALCIUM ION × 7 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；289 K；PEG 8000,Ammonium sulfate,sodium citrate	Resolution 1.10 Å R-free 0.186

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 5D7W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AF0 SERRATIA PROTEASE IN COMPLEX WITH INHIBITOR Deposited 1997-03-20	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 A 17–487（471 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 7 0Z9 N-[(benzyloxy)carbonyl]-L-leucyl-N-hydroxy-L-alaninamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2 M AMMONIUM SULFATE, 20%PEG 4K, PH 6.5	Resolution 1.80 Å
1SAT CRYSTAL STRUCTURE OF THE 50 KDA METALLO PROTEASE FROM S. MARCESCENS Deposited 1994-07-04	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 A 17–487（471 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 7	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.75 Å
1SMP CRYSTAL STRUCTURE OF A COMPLEX BETWEEN SERRATIA MARCESCENS METALLO-PROTEASE AND AN INHIBITOR FROM ERWINIA CHRYSANTHEMI Deposited 1995-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–487（471 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 7	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.247

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRZN_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–469； UniProt 20–487

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	5d7w
Deposition date deposition_date	2015-08-14
Structure title title	Crystal structure of serralysin
Keywords keywords	protease, metalloprotease, HYDROLASE; HYDROLASE
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	26.34 Å
Radius of gyration Rg (electron density) rg_electron	26.08 Å
Forward intensity I(0) i0	45934100.00
Molecular weight molecular_weight	50732.0 kDa
Excluded volume excluded_volume	62356 Å³
Envelope volume envelope_volume	73171 Å³
Hydration-shell volume shell_volume	25033 Å³
Envelope diameter envelope_diameter	97.5 Å
Shell Rg shell_rg	31.52 Å
Envelope Rg envelope_rg	26.59 Å
Shape Rg shape_rg	26.09 Å
Total Rg total_rg	26.57 Å
Total atoms total_atoms	3581
Residues n_residues	469
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	94.1 Å
Rg (real space) rg_real	26.60 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	4.5930e+07
I(0) uncertainty (real space) i0_real_error	6.6400e+05
Rg (reciprocal space) rg_reciprocal	26.52 Å
I(0) (reciprocal space) i0_reciprocal	45930000.0000
Solution quality estimate total_estimate	0.8141
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.635
Kurtosis Kurtosis kurtosis	-0.003
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6947000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.629; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.732; Smooth: 0.961

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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	Serralysin
Molecular weight formula_weight	50267.0 kDa
EC 编号 ec_number	3.4.24.40
Mutation mutation	P250L
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	4400

ATGYDAVDDLLHYHERGNGIQINGKDSFSNEQAGLFITRENQTWNGYKVFGQPVKLTFSFPDYKFSSTNVAGDTGLSKFSAEQQQQAKLSLQSWADVANITFTEVAAGQKANITFGNYSQDRPGHYDYGTQAYAFLPNTIWQGQDLGGQTWYNVNQSNVKHPATEDYGRQTFTHEIGHALGLSHPGDYNAGEGNPTYNDVTYAEDTRQFSLMSYWSETNTGGDNGGHYAAAPLLDDIAAIQHLYGANLSTRTGDTVYGFNSNTGRDFLSTTSNSQKVIFAAWDAGGNDTFDFSGYTANQRINLNEKSFSDVGGLKGNVSIAAGVTIENAIGGSGNDVIVGNAANNVLKGGAGNDVLFGGGGADELWGGAGKDIFVFSAASDSAPGASDWIRDFQKGIDKIDLSFFNKEANSSDFIHFVDHFSGTAGEALLSYNASSNVTDLSVNIGGHQAPDFLVKIVGQVDVATDFIV

来源 Source

来源生物 organism	Serratia marcescens
NCBI Class编号 ncbi_taxonomy_id	615
宿主生物 host_organism	Serratia

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	696

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5d7wa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.0 — automated matches

Domain ID domain_id	d5d7wa2
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.7 — beta-Roll
Family Family family	b.80.7.0 — automated matches

Domain ID domain_id	d5d7wa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5d7wA01
Class class	2 — Mainly Beta
Architecture architecture	150 — 2 Solenoid
Topology topology	10 — Alkaline Protease, subunit P, domain 1
Homologous superfamily homologous superfamily	10 — Serralysin-like metalloprotease, C-terminal

Domain ID domain_id	5d7wA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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8. Citations (1)

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Unit-cell length a length_a	42.300 Å
Unit-cell length b length_b	105.400 Å
Unit-cell length c length_c	151.100 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	4

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

Resolution resolution	1.100 Å
Low-resolution limit resolution_low	19.628 Å
R factor r_factor	0.1759
R_work r_work	0.1754
R_free r_free	0.1861

fit	/app/data/saxs_computation/d7/5d7w/5d7w.fit
pddf	/app/data/pr_computation/d7/5d7w/5d7w.pr.out
profile	/app/data/saxs_computation/d7/5d7w/5d7w.dat

Crystal structure of serralysin

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

Serralysin

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