SAXSdb — 4cfz

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

SUBTILISIN SAVINASE

BACILLUS LENTUS

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 1–269	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：CRYSTALS FROM INDUSTRIAL PRODUCTION SUSPENSION	Resolution 1.57 Å R-free 0.180

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 4CFZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C9J BACILLUS LENTUS SUBTILISIN K27R/N87S/V104Y/N123S/T274A VARIANT Deposited 1999-08-02	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 1–269（269 aa）	Mutation：K27R, N87S, V104Y, N123S, T274A	SO4 SULFATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；SODIUM ACATEATE, CALCIUM CHLORIDE, AMMONIUM SULFATE, pH 5.9, VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å
1C9M BACILLUS LENTUS SUBTILSIN (SER 87) N76D/S103A/V104I Deposited 1999-08-02	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 1–269（269 aa）	Mutation：N76D, S103A, V104I FROM NATIVE (SER 87) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；SODIUM ACTETATE, CALCIUM CHLORIDE, AMMONIUM SULFATE ,PHENYLMETHYLSULFANYL- FLOURIDE, pH 5.9, VAPOR DIFFUSION, HANGING DROP	Resolution 1.67 Å
1C9N BACILLUS LENTUS SUBSTILISIN VARIANT (SER 87) K27R/V104Y/N123S/T274A Deposited 1999-08-02	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 1–269（269 aa）	Mutation：K27R, V104Y, N123S, T274A FROM NATIVE (SER 87)	SO4 SULFATE ION × 1 CA CALCIUM ION × 2 PMS phenylmethanesulfonic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；SODIUM ACETATE, CALCIUM CHLORIDE, AMMONIUM SULFATE, pH 5.9, VAPOR DIFFUSION, HANGING DROP	Resolution 1.50 Å
1GCI THE 0.78 ANGSTROMS STRUCTURE OF A SERINE PROTEASE-BACILLUS LENTUS SUBTILISIN Deposited 1998-09-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–269（269 aa）	Not recorded	SO4 SULFATE ION × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.9；FREE TEXT GOES HERE., pH 5.9	Resolution 0.78 Å R-free 0.103
1IAV STRUCTURE ON NATIVE (ASN 87) SUBTILISIN FROM BACILLUS LENTUS Deposited 2001-03-23	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 1–269（269 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.9；pH 5.90	Resolution 1.80 Å
1JEA ALTERED TOPOLOGY AND FLEXIBILITY IN ENGINEERED SUBTILISIN Deposited 1997-05-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–269（269 aa）	Not recorded	CA CALCIUM ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1NDQ Bacillus lentus subtilisin Deposited 2002-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–269（269 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.229
1NDU Bacillus lentus subtilisin variant S101G/V104N Deposited 2002-12-09	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 1–269（269 aa）	Mutation：S101G, V104N	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.222
1Q5P S156E/S166D variant of Bacillus lentus subtilisin Deposited 2003-08-08	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 1–269（269 aa）	Mutation：S156E, S166D Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
1SVN SAVINASE Deposited 1995-09-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–269（269 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å
1TK2 Crystal Structure of the Complex formed between Alkaline Proteinase Savinase and Gramicidin S at 1.5A Resolution Deposited 2004-06-08	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 1–269（269 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.33M NACL, 10% PEG 4000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K	Resolution 1.54 Å R-free 0.189
3BX1 Complex between the Barley alpha-Amylase/Subtilisin Inhibitor and the subtilisin Savinase Deposited 2008-01-11	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 1–269（269 aa）	Not recorded	CA CALCIUM ION × 2 CL CHLORIDE ION × 15 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1 M sodium acetate buffer pH 5.6 and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.239
3BX1 Complex between the Barley alpha-Amylase/Subtilisin Inhibitor and the subtilisin Savinase Deposited 2008-01-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–269（269 aa）	Not recorded	CA CALCIUM ION × 2 CL CHLORIDE ION × 9 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1 M sodium acetate buffer pH 5.6 and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.239
3BX1 Complex between the Barley alpha-Amylase/Subtilisin Inhibitor and the subtilisin Savinase Deposited 2008-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–269（269 aa） Chain B 1–269（269 aa）	Not recorded	CA CALCIUM ION × 8 CL CHLORIDE ION × 48 NA SODIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1 M sodium acetate buffer pH 5.6 and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.239
4CFY SAVINASE CRYSTAL STRUCTURES FOR COMBINED SINGLE CRYSTAL DIFFRACTION AND POWDER DIFFRACTION ANALYSIS Deposited 2013-11-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–269（269 aa）	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20 MG/ML PROTEIN, 4% PEG 4000, 0.33 M NACL, 1.5 MM CACL2, 18 MM CITRATE BUFFER PH 6.0	Resolution 1.17 Å R-free 0.119
4CG0 Savinase crystal structures for combined single crystal diffraction and powder diffraction analysis Deposited 2013-11-19	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–269（269 aa）	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions CRYSTALS FROM INDUSTRIAL PRODUCTION SUSPENSION	Resolution 1.36 Å R-free 0.154
5AQE Cooperative bio-metallic selectivity in a tailored protease enables creation of a C-C cross-coupling Heckase Deposited 2015-09-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–269（269 aa） Fragment：MATURE PEPTIDE CHAIN	Not recorded	VOD (4-VINYLPHENYL)METHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 9% PEG 3350, 50 MM AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5	Resolution 1.10 Å R-free 0.088
5ARB Cooperative bio-metallic selectivity in a tailored protease enables creation of a C-C cross-coupling Heckase Deposited 2015-09-24	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 1–269（269 aa） Fragment：MATURE PEPTIDE CHAIN, RESIDUES 1-269	Mutation：YES	CA CALCIUM ION × 1 GOL GLYCEROL × 3 EI3 5-methyl-2-(5-methylpyridin-2-yl)pyridine × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 15% PEG 3350, 75 MM AMMONIUM SULPHATE, 0.1 M BIS TRIS PH 5.5	Resolution 1.15 Å R-free 0.121
5ARC Cooperative bio-metallic selectivity in a tailored protease enables creation of a C-C cross-coupling Heckase Deposited 2015-09-24	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 1–269（269 aa） Fragment：MATURE PEPTIDE CHAIN, RESIDUES 1-269	Mutation：YES	CA CALCIUM ION × 1 EI3 5-methyl-2-(5-methylpyridin-2-yl)pyridine × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；25% PEG 3350, 100 MM AMMONIUM SULPHATE, 0.1 M BIS TRIS PROPANE PH 8.5	Resolution 1.10 Å R-free 0.123
5ARD Cooperative bio-metallic selectivity in a tailored protease enables creation of a C-C cross-coupling Heckase Deposited 2015-09-24	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 1–269（269 aa） Fragment：MATURE PEPTIDE CHAIN, RESIDUES 1-269	Mutation：YES	CA CALCIUM ION × 1 GOL GLYCEROL × 2 EI3 5-methyl-2-(5-methylpyridin-2-yl)pyridine × 1 NI NICKEL (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；33% PEG 3350, 100 MM AMMONIUM SULFATE, 0.1 M TRIS PH 7.5	Resolution 1.55 Å R-free 0.154
6Y5S Crystal structure of savinase at cryogenic conditions Deposited 2020-02-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–269（269 aa）	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.2 M NaBr, 0.1 M Bis Tris propane, 20% PEG3350	Resolution 0.95 Å R-free 0.155
6Y5T Crystal structure of savinase at room temperature Deposited 2020-02-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–269（269 aa）	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.2 M NaBr, 0.1 M Bis Tris propane, 20% PEG3350	Resolution 1.10 Å R-free 0.150

20 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SUBS_BACLE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–269； UniProt 1–269

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	4cfz
Deposition date deposition_date	2013-11-19
Structure title title	SAVINASE CRYSTAL STRUCTURES FOR COMBINED SINGLE CRYSTAL DIFFRACTION AND POWDER DIFFRACTION ANALYSIS
Keywords keywords	HYDROLASE, SINGLE CRYSTAL ANALYSIS, POWDER DIFFRACTION, QUALITY CONTROL, MICROCRYSTALLINE SUSPENSION; 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	17.82 Å
Radius of gyration Rg (electron density) rg_electron	16.40 Å
Forward intensity I(0) i0	15194300.00
Molecular weight molecular_weight	27151.0 kDa
Excluded volume excluded_volume	33001 Å³
Envelope volume envelope_volume	36107 Å³
Hydration-shell volume shell_volume	17922 Å³
Envelope diameter envelope_diameter	52.3 Å
Shell Rg shell_rg	23.10 Å
Envelope Rg envelope_rg	16.61 Å
Shape Rg shape_rg	16.37 Å
Total Rg total_rg	17.39 Å
Total atoms total_atoms	1899
Residues n_residues	269
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	52.5 Å
Rg (real space) rg_real	17.64 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	1.5190e+07
I(0) uncertainty (real space) i0_real_error	1.5400e+05
Rg (reciprocal space) rg_reciprocal	17.66 Å
I(0) (reciprocal space) i0_reciprocal	15190000.0000
Solution quality estimate total_estimate	0.9047
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	-0.002
Kurtosis Kurtosis kurtosis	-0.547
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4129000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.991

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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	SUBTILISIN SAVINASE
Molecular weight formula_weight	26718.4 kDa
EC 编号 ec_number	3.4.21.62
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	2242

AQSVPWGISRVQAPAAHNRGLTGSGVKVAVLDTGISTHPDLNIRGGASFVPGEPSTQDGNGHGTHVAGTIAALNNSIGVLGVAPSAELYAVKVLGASGSGSVSSIAQGLEWAGNNGMHVANLSLGSPSPSATLEQAVNSATSRGVLVVAASGNSGAGSISYPARYANAMAVGATDQNNNRASFSQYGAGLDIVAPGVNVQSTYPGSTYASLNGTSMATPHVAGAAALVKQKNPSWSNVQIRNHLKNTATSLGSTNLYGSGLVNAEAATR

来源 Source

来源生物 organism	BACILLUS LENTUS
NCBI Class编号 ncbi_taxonomy_id	1467
宿主生物 host_organism	BACILLUS LICHENIFORMIS

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	269

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4cfza_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.41 — Subtilisin-like
Superfamily Superfamily superfamily	c.41.1 — Subtilisin-like
Family Family family	c.41.1.1 — Subtilases

CATH v4.4 (1 domains)

Domain ID domain_id	4cfzA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	200 — Peptidase S8/S53 domain

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8. Citations (1)

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Unit-cell length a length_a	52.720 Å
Unit-cell length b length_b	57.130 Å
Unit-cell length c length_c	65.860 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	1.570 Å
Low-resolution limit resolution_low	23.940 Å
R factor r_factor	0.1406
R_work r_work	0.1386
R_free r_free	0.1797

fit	/app/data/saxs_computation/cf/4cfz/4cfz.fit
pddf	/app/data/pr_computation/cf/4cfz/4cfz.pr.out
profile	/app/data/saxs_computation/cf/4cfz/4cfz.dat

SAVINASE CRYSTAL STRUCTURES FOR COMBINED SINGLE CRYSTAL DIFFRACTION AND POWDER DIFFRACTION ANALYSIS

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

SUBTILISIN SAVINASE

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