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1c9j

BACILLUS LENTUS SUBTILISIN K27R/N87S/V104Y/N123S/T274A VARIANT

Method: X-RAY DIFFRACTION Dmax: 60.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SERINE PROTEASE

Bacillus lentus

UniProt P29600

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：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

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 1C9J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C9M BACILLUS LENTUS SUBTILSIN (SER 87) N76D/S103A/V104I 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：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 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 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.

SAXS scattering curve SAXS Profile

SAXS profile for 1c9j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c9j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1c9j
Deposition date deposition_date1999-08-02
Structure title titleBACILLUS LENTUS SUBTILISIN K27R/N87S/V104Y/N123S/T274A VARIANT
Keywords keywordsSUBTILISIN, HYDROLASE, ALTERED FLEXIBILITY; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.63 Å
Radius of gyration Rg (electron density) rg_electron16.38 Å
Forward intensity I(0) i014340000.00
Molecular weight molecular_weight26913.0 kDa
Excluded volume excluded_volume32979 ų
Envelope volume envelope_volume35800 ų
Hydration-shell volume shell_volume17840 ų
Envelope diameter envelope_diameter51.9 Å
Shell Rg shell_rg22.97 Å
Envelope Rg envelope_rg16.52 Å
Shape Rg shape_rg16.38 Å
Total Rg total_rg17.29 Å
Total atoms total_atoms1890
Residues n_residues269
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax60.1 Å
Rg (real space) rg_real17.46 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real1.4340e+07
I(0) uncertainty (real space) i0_real_error1.5640e+05
Rg (reciprocal space) rg_reciprocal17.48 Å
I(0) (reciprocal space) i0_reciprocal14340000.0000
Solution quality estimate total_estimate0.7746
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.0 Å
Skewness Skewness skewness-0.013
Kurtosis Kurtosis kurtosis-0.542
Angular range angular_range— – 0.4500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4241000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.689; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1c9ja_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.41 — Subtilisin-like
Superfamily Superfamily superfamilyc.41.1 — Subtilisin-like
Family Family familyc.41.1.1 — Subtilases

CATH v4.4 (1 domains)

Domain ID domain_id1c9jA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily200 — Peptidase S8/S53 domain
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8. Citations (1)

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9. Files and Curves (10)