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- PDB-4gpg: X/N joint refinement of Achromobacter Lyticus Protease I free for... -

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Basic information

Entry
Database: PDB / ID: 4gpg
TitleX/N joint refinement of Achromobacter Lyticus Protease I free form at pD8.0
ComponentsProtease 1
KeywordsHYDROLASE / lysine specific serine protease
Function / homology
Function and homology information


lysyl endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Lysyl endopeptidase / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins ...Lysyl endopeptidase / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Galactose-binding-like domain superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DEUTERATED WATER / Protease 1
Similarity search - Component
Biological speciesAchromobacter lyticus (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 1.895 Å
AuthorsOhnishi, Y. / Yamada, T. / Kurihara, K. / Tanaka, I. / Sakiyama, F. / Masaki, T. / Niimura, N.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Neutron and X-ray crystallographic analysis of Achromobacter protease I at pD 8.0: protonation states and hydration structure in the free-form.
Authors: Ohnishi, Y. / Yamada, T. / Kurihara, K. / Tanaka, I. / Sakiyama, F. / Masaki, T. / Niimura, N.
History
DepositionAug 21, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.details / _diffrn_detector.type ..._diffrn_detector.details / _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.2Nov 20, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 4, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.d_res_low
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease 1


Theoretical massNumber of molelcules
Total (without water)27,7591
Polymers27,7591
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.574, 40.785, 43.980
Angle α, β, γ (deg.)64.82, 66.10, 73.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protease 1 / API / Lysyl endopeptidase / Protease I


Mass: 27759.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter lyticus (bacteria) / Strain: M497-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15636, lysyl endopeptidase
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 8
Details: 20% w/v PEG 3350, 10mM Tris, HCl pH 8.0, 50% PEG 3350, HCl pD 8.0, VAPOR DIFFUSION, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12971
22971
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORJRR-3M 1G-C12.6
ROTATING ANODEMACSCIENCE M06X21.5418
Detector
TypeIDDetectorDateDetails
1IMAGE PLATEJun 12, 2007BIX-4, SILICON
MAC Science DIP-20002IMAGE PLATEMay 1, 2007double mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SILICON(111)SINGLE WAVELENGTHMneutron1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
12.61
21.54181
Reflection

Entry-ID: 4GPG / Observed criterion σ(I): _ / % possible obs: 89.4 %

Resolution (Å)Num. obsObserved criterion σ(F)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.98-501100000.16114.87
1.895-50161280.078217.38
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.88-1.950.1985.95289.4
1.95-2.030.177.2289.8
2.03-2.120.1359.3290.2
2.12-2.230.12110.5291.1
2.23-2.370.11211.6290.5
2.37-2.550.09913291.3
2.55-2.810.08615.3291.6
2.81-3.210.07517.8292.2
3.21-4.050.06223292.6
4.05-800.06223.3294.4
2-2.070.3192.5246
2.07-2.150.3422.9252.9
2.15-2.250.333.2257.9
2.25-2.370.3292.9262.5
2.37-2.520.2883.3266.3
2.52-2.710.2893.7272.1
2.71-2.990.2474.5281.8
2.99-3.420.186.7291
3.42-4.310.1399.7296.6
4.31-500.12410.7298.1
2-2.070.3192.51146

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Processing

Software
NameVersionClassification
MacSciencexdipdata collection
PHENIX(phenix.refine: 1.7.3_911)refinement
DENZOdata reduction
SCALEPACKdata scaling
Refinement

Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Starting modelResolution (Å)Refine-IDBaniso 11 (Å2)Baniso 12 (Å2)Baniso 13 (Å2)Baniso 22 (Å2)Baniso 23 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Occupancy maxOccupancy minSU MLDiffraction-IDσ(F)Phase errorShrinkage radii (Å)VDW probe radii (Å)
1ARC

1arc

1.895-20.358X-RAY DIFFRACTION-2.33751.76762.59664.4118-2.9931-2.07430.20280.14660.1493800160814.9789.99100.1722.0823.2400.6
1.979-37.61NEUTRON DIFFRACTION-0.058-1.33270.8508-1.29850.8387-3.45690.25950.19520.1984554109985.0469.970.32123.660.81
Refinement stepCycle: LAST / Resolution: 1.895→20.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 0 140 2060
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0114181
NEUTRON DIFFRACTIONf_angle_d1.4737299
NEUTRON DIFFRACTIONf_dihedral_angle_d16.3151022
NEUTRON DIFFRACTIONf_chiral_restr0.096289
NEUTRON DIFFRACTIONf_plane_restr0.007887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8953-2.01390.31151300.23992306X-RAY DIFFRACTION82
2.0139-2.16920.28211280.19392574X-RAY DIFFRACTION90
2.1692-2.38720.21591340.16132562X-RAY DIFFRACTION91
2.3872-2.7320.23131280.1522590X-RAY DIFFRACTION92
2.732-3.43930.20021380.13492610X-RAY DIFFRACTION92
3.4393-20.35880.15021420.12032639X-RAY DIFFRACTION93
1.979-2.17810.3745870.31831597NEUTRON DIFFRACTION43
2.1781-2.49320.33951190.24492315NEUTRON DIFFRACTION62
2.4932-3.14090.2791550.18592945NEUTRON DIFFRACTION79
3.1409-37.6170.17911930.13533587NEUTRON DIFFRACTION96

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