SAXSdb — 1c9m

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

SERINE PROTEASE

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	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

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 1C9M	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 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
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 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）	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 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 mutation/modification 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 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）	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 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 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）	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 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 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 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 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 mutation/modification 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 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）	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
4CFZ SAVINASE CRYSTAL STRUCTURES FOR COMBINED SINGLE CRYSTAL DIFFRACTION AND POWDER DIFFRACTION ANALYSIS Deposited 2013-11-19	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）	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
4CG0 Savinase crystal structures for combined single crystal diffraction and powder diffraction analysis Deposited 2013-11-19	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）	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 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	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 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）	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 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）	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	1c9m
Deposition date deposition_date	1999-08-02
Structure title title	BACILLUS LENTUS SUBTILSIN (SER 87) N76D/S103A/V104I
Keywords keywords	SERINE PROTEASE, SUBTILISIN, SITE-SPECIFIC VARIANT, ALTERED FLEXIBILITY, 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	17.56 Å
Radius of gyration Rg (electron density) rg_electron	16.30 Å
Forward intensity I(0) i0	14375600.00
Molecular weight molecular_weight	27031.0 kDa
Excluded volume excluded_volume	33163 Å³
Envelope volume envelope_volume	35633 Å³
Hydration-shell volume shell_volume	17818 Å³
Envelope diameter envelope_diameter	52.1 Å
Shell Rg shell_rg	22.96 Å
Envelope Rg envelope_rg	16.46 Å
Shape Rg shape_rg	16.30 Å
Total Rg total_rg	17.23 Å
Total atoms total_atoms	1897
Residues n_residues	268
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	51.0 Å
Rg (real space) rg_real	17.39 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	1.4380e+07
I(0) uncertainty (real space) i0_real_error	1.4900e+05
Rg (reciprocal space) rg_reciprocal	17.41 Å
I(0) (reciprocal space) i0_reciprocal	14380000.0000
Solution quality estimate total_estimate	0.8079
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	-0.014
Kurtosis Kurtosis kurtosis	-0.517
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3802000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 0.966; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	SERINE PROTEASE
Molecular weight formula_weight	26871.6 kDa
EC 编号 ec_number	3.4.21.62
Mutation mutation	N76D, S103A, V104I FROM NATIVE (SER 87)
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	2001

AQSVPWGISRVQAPAAHNRGLTGSGVKVAVLDTGISTHPDLNIRGGASFVPGEPSTQDGNGHGTHVAGTIAALDNSIGVLGVAPSAELYAVKVLGASGSGAISSIAQGLEWAGNNGMHVANLSLGSPSPSATLEQAVNSATSRGVLVVAASGNSGAGSISYPARYANAMAVGATDQNNNRASFSQYGAGLDIVAPGVNVQSTYPGSTYASLNGTSMATPHVAGAAALVKQKNPSWSNVQIRNHLKNTATSLGSTNLYGSGLVNAEAATR

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 subtilis

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c9ma_
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	1c9mA00
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	53.250 Å
Unit-cell length b length_b	61.250 Å
Unit-cell length c length_c	75.050 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	1.670 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1680
R_work r_work	0.1680
R_free r_free	—

fit	/app/data/saxs_computation/c9/1c9m/1c9m.fit
pddf	/app/data/pr_computation/c9/1c9m/1c9m.pr.out
profile	/app/data/saxs_computation/c9/1c9m/1c9m.dat

BACILLUS LENTUS SUBTILSIN (SER 87) N76D/S103A/V104I