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- PDB-2oua: Crystal Structure of Nocardiopsis Protease (NAPase) -

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Basic information

Entry
Database: PDB / ID: 2oua
TitleCrystal Structure of Nocardiopsis Protease (NAPase)
ComponentsSerine protease
Keywordshydrolase/hydrolase inhibitor / serine protease / kinetic stability / acid stability / electrostatics / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


serine-type endopeptidase activity / extracellular region
Similarity search - Function
Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan ...Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin domain / Trypsin / 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
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / 1,4-DIETHYLENE DIOXIDE / Serine protease
Similarity search - Component
Biological speciesNocardiopsis alba (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKelch, B.A. / Agard, D.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and mechanistic exploration of Acid resistance: kinetic stability facilitates evolution of extremophilic behavior
Authors: Kelch, B.A. / Eagen, K.P. / Erciyas, F.P. / Humphris, E.L. / Thomason, A.R. / Mitsuiki, S. / Agard, D.A.
History
DepositionFeb 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 6, 2012Group: Non-polymer description
Revision 1.4Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Serine protease
B: Serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,43712
Polymers38,2982
Non-polymers1,13910
Water6,882382
1
A: Serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9058
Polymers19,1491
Non-polymers7567
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5324
Polymers19,1491
Non-polymers3833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.605, 61.605, 184.479
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological unit is monomer. There are 2 biological units in the asymmetric unit.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serine protease / / protein napA


Mass: 19148.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: gene napA / Source: (natural) Nocardiopsis alba (bacteria) / Secretion: YES / Strain: TOA-1 / References: UniProt: Q6K1C5

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Non-polymers , 5 types, 392 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF / AEBSF


Mass: 203.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.3M ammonium sulfate, 10%(v/v) dioxane, 0.1M MES, pH 6.0, 10mg/ml NAPase, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 13, 2005
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→46.18 Å / Num. all: 35653 / Num. obs: 34991 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 6.2 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.66
Reflection shellHighest resolution: 1.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.91 / Num. unique all: 1748 / % possible all: 98.7

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-Ala model of TFPA (to be submitted)

Resolution: 1.85→46.18 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1662 -random
Rwork0.1759 ---
all-35653 --
obs-33592 94.2 %-
Displacement parametersBiso mean: 12.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 70 382 3112
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_mcbond_it1.0281.5
X-RAY DIFFRACTIONx_mcangle_it1.462
X-RAY DIFFRACTIONx_scbond_it1.8342
X-RAY DIFFRACTIONx_scangle_it2.6412.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.236 251 -
Rwork0.2 --
obs-5020 90.7 %

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