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- PDB-4h6w: Structure of Prenylagaramide maturation protease PagA -

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Basic information

Entry
Database: PDB / ID: 4h6w
TitleStructure of Prenylagaramide maturation protease PagA
ComponentsN-terminal cyanobactin protease
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


serine-type endopeptidase activity
Similarity search - Function
Peptidase S8A, PatG / PatG/PatA-like domain / PatG domain / PatG, C-terminal / PatG Domain / PatG C-terminal / Peptidase S8/S53 domain / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related ...Peptidase S8A, PatG / PatG/PatA-like domain / PatG domain / PatG, C-terminal / PatG Domain / PatG C-terminal / Peptidase S8/S53 domain / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-terminal cyanobactin protease
Similarity search - Component
Biological speciesPlanktothrix agardhii NIES-596 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsNair, S.K. / Agarwal, V.
CitationJournal: Chem.Biol. / Year: 2012
Title: Structures of cyanobactin maturation enzymes define a family of transamidating proteases.
Authors: Agarwal, V. / Pierce, E. / McIntosh, J. / Schmidt, E.W. / Nair, S.K.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-terminal cyanobactin protease
B: N-terminal cyanobactin protease


Theoretical massNumber of molelcules
Total (without water)64,1772
Polymers64,1772
Non-polymers00
Water2,810156
1
A: N-terminal cyanobactin protease


Theoretical massNumber of molelcules
Total (without water)32,0881
Polymers32,0881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-terminal cyanobactin protease


Theoretical massNumber of molelcules
Total (without water)32,0881
Polymers32,0881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.700, 145.930, 193.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein N-terminal cyanobactin protease


Mass: 32088.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planktothrix agardhii NIES-596 (bacteria)
Gene: pagA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: F5B6Y7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: PEG 20000, vapor diffusion, hanging drop, temperature 281K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 24491 / % possible obs: 93.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Χ2: 0.983 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.45-2.543.50.49117290.741167.2
2.54-2.644.10.41620530.77178.9
2.64-2.764.80.36223240.786189.9
2.76-2.95.40.29725170.805197
2.9-3.095.90.21826000.817199.4
3.09-3.326.10.13825810.829199.5
3.32-3.666.10.08825790.884199.8
3.66-4.1960.06526471.24199.9
4.19-5.2860.05226651.478199.9
5.28-505.60.03427961.103199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.222 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.387 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 1235 5 %RANDOM
Rwork0.1867 ---
obs0.189 24490 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 138.13 Å2 / Biso mean: 47.672 Å2 / Biso min: 22.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å2-0 Å2
2--1.42 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.45→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 0 156 4208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194122
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9785609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.3126.282156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29515687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3241514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213064
LS refinement shellResolution: 2.455→2.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 57 -
Rwork0.283 1112 -
all-1169 -
obs--61.43 %

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