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- PDB-3cp7: Crystal structure of a thermostable serine protease AL20 from ext... -

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Basic information

Entry
Database: PDB / ID: 3cp7
TitleCrystal structure of a thermostable serine protease AL20 from extremophilic microoganism
Componentsalkaline serine protease AL20
KeywordsHYDROLASE / trypsin-like
Function / homology
Function and homology information


chymotrypsin / serine-type endopeptidase activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #400 / : / Trypsin-like peptidase domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #400 / : / Trypsin-like peptidase domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Alkaline serine protease AL20
Similarity search - Component
Biological speciesNesterenkonia abyssinica
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsYang, N. / Nan, J. / Su, X.-D.
Citation
Journal: Proteins / Year: 2008
Title: Crystal structure of an alkaline serine protease from Nesterenkonia sp. defines a novel family of secreted bacterial proteases
Authors: Yang, N. / Nan, J. / Brostromer, E. / Hatti-Kaul, R. / Su, X.-D.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Crystallization and preliminary X-ray analysis of an alkaline serine protease from Nesterenkonia sp.
Authors: Bakhtiar, S. / Hatti-Kaul, R. / Su, X.D.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 AL20
B: alkaline serine protease AL20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9854
Polymers45,8932
Non-polymers922
Water11,836657
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-4.5 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.260, 92.260, 137.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-570-

HOH

21B-681-

HOH

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Components

#1: Protein alkaline serine protease AL20


Mass: 22946.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nesterenkonia abyssinica / References: UniProt: D0VWT7*PLUS, chymotrypsin
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2.9M sodium formate, 0.1M sodium citrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.076 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 1, 2002 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.076 Å / Relative weight: 1
ReflectionResolution: 1.39→19.8 Å / Num. all: 88125 / Num. obs: 86325 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.16 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.047 / Net I/σ(I): 14.5
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 3.5 / Num. unique all: 8921 / Rsym value: 0.193 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P3E

1p3e


Resolution: 1.39→19.18 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.911 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19904 2161 2.5 %RANDOM
Rwork0.17834 ---
all0.17887 86325 --
obs0.17887 84142 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.788 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.39→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 0 663 3871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213316
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.8964524
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03325168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09115396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.435156
X-RAY DIFFRACTIONr_chiral_restr0.1740.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022738
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21632
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22312
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2563
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.259
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6161.52153
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06823358
X-RAY DIFFRACTIONr_scbond_it1.4931330
X-RAY DIFFRACTIONr_scangle_it2.1834.51166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.392→1.428 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 157 -
Rwork0.261 5778 -
obs-5778 100 %

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