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- PDB-8h7p: Crystal structure of aqualigase bound with Suc-AAPF -

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Basic information

Entry
Database: PDB / ID: 8h7p
TitleCrystal structure of aqualigase bound with Suc-AAPF
Components
  • 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
  • Subtilisin
KeywordsHYDROLASE / subtilisin / Ser protease / structure based engineering / peptide synthesis
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
: / Fervidolysin N-terminal prodomain / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...: / Fervidolysin N-terminal prodomain / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Peptidase S8
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLi, H. / Ma, M.Z. / Zhang, L.J. / Dai, L. / Chen, C.-C. / Guo, R.-T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of aqualigase bound with Suc-AAPF
Authors: Li, H. / Ma, M.Z. / Zhang, L.J. / Dai, L. / Chen, C.-C. / Guo, R.-T.
History
DepositionOct 20, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilisin
B: 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0564
Polymers28,8662
Non-polymers1902
Water3,837213
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint4 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.578, 71.680, 40.804
Angle α, β, γ (deg.)90.000, 114.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Subtilisin


Mass: 28363.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: KS08_04965 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A7U5AV24, subtilisin
#2: Protein/peptide 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE


Mass: 502.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.68 Å3/Da / Density % sol: 26.96 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 25% isopropanol, 28% PEG 3350, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.82→37.06 Å / Num. obs: 17217 / % possible obs: 97.3 % / Redundancy: 4.8 % / CC1/2: 0.997 / Net I/σ(I): 20.8
Reflection shellResolution: 1.82→1.85 Å / Num. unique obs: 806 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TO1

1to1


Resolution: 1.82→37.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.1969 / WRfactor Rwork: 0.1412 / FOM work R set: 0.8876 / SU B: 2.957 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1609 / SU Rfree: 0.1405 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 842 5.3 %RANDOM
Rwork0.1352 ---
obs0.138 14907 91.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.11 Å2 / Biso mean: 10.87 Å2 / Biso min: 5.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å20.22 Å2
2--0.47 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.82→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 47 213 2256
Biso mean--15.96 22.37 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132100
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171887
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.6342865
X-RAY DIFFRACTIONr_angle_other_deg1.5221.5944404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78225.06873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58415296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.058152
X-RAY DIFFRACTIONr_chiral_restr0.0750.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
LS refinement shellResolution: 1.82→1.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 52 -
Rwork0.191 1050 -
all-1102 -
obs--87.39 %

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