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- PDB-1wvm: Crystal Structure of Psychrophilic Subtilisin-like Serine Proteas... -

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Basic information

Entry
Database: PDB / ID: 1wvm
TitleCrystal Structure of Psychrophilic Subtilisin-like Serine Protease APA1 from Antarctic Psychrotroph Pseudoaleromonas sp. AS-11, Complexed with Inhibitor Chymostatin
Components
  • CHYMOSTATIN
  • alkaline serine protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / subtilisin-like alpha/beta domain / insert beta barrel domain / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Glucose Oxidase; domain 1 - #30 / PA domain / PA domain / Subtilisin Carlsberg-like catalytic domain / Glucose Oxidase; domain 1 ...P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Glucose Oxidase; domain 1 - #30 / PA domain / PA domain / Subtilisin Carlsberg-like catalytic domain / Glucose Oxidase; domain 1 / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Galactose-binding-like domain superfamily / 3-Layer(bba) Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chymostatin A / : / Alkaline serine protease
Similarity search - Component
Biological speciesPseudoalteromonas sp. (bacteria)
Streptomyces hygroscopicus (bacteria)
MC521-C8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDong, D. / Watanabe, K.
CitationJournal: To be Published
Title: Crystal Structure of Psychrophilic Subtilisin-like Serine Protease from Antarctic Psychrotroph Pseudoalteromonas sp. AS-11 at 0.16 nm resolution
Authors: Dong, D. / Watanabe, K.
History
DepositionDec 16, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 2.0Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alkaline serine protease
B: alkaline serine protease
C: CHYMOSTATIN
D: CHYMOSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,86816
Polymers91,5134
Non-polymers35512
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: alkaline serine protease
B: alkaline serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,65314
Polymers90,2982
Non-polymers35512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: alkaline serine protease
D: CHYMOSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9589
Polymers45,7572
Non-polymers2027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-55 kcal/mol
Surface area15680 Å2
MethodPISA
4
A: alkaline serine protease
C: CHYMOSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9107
Polymers45,7572
Non-polymers1535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-52 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.230, 138.340, 64.880
Angle α, β, γ (deg.)90.00, 97.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-614-

MG

21A-841-

HOH

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Components

#1: Protein alkaline serine protease / subtilisin-like protease


Mass: 45149.031 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-441 / Source method: isolated from a natural source / Details: Extracellular Enzyme / Source: (natural) Pseudoalteromonas sp. (bacteria) / Strain: AS-11
References: GenBank: 52421107, UniProt: Q65Z69*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide CHYMOSTATIN


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 607.701 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces hygroscopicus, MC521-C8 / References: Chymostatin A
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG5000MME, 0.1M magnisium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2004
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→34.59 Å / Num. all: 136680 / Num. obs: 134538 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.241 / Num. unique all: 11185 / % possible all: 79.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V6C

1v6c


Resolution: 1.6→34.59 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 250168.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 13440 10 %RANDOM
Rwork0.192 ---
obs0.192 134538 95 %-
all-136680 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5917 Å2 / ksol: 0.357135 e/Å3
Displacement parametersBiso mean: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å21.47 Å2
2--1.26 Å20 Å2
3----2.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å-0.01 Å
Refinement stepCycle: LAST / Resolution: 1.6→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6353 0 12 538 6903
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it0.891.5
X-RAY DIFFRACTIONc_mcangle_it1.312
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.182.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.233 1923 10 %
Rwork0.208 17400 -
obs-19323 82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4CHY.PARAMCHY.TOP

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