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- PDB-6ah8: Marine bacterial prolidase with promiscuous organophosphorus hydr... -

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Basic information

Entry
Database: PDB / ID: 6ah8
TitleMarine bacterial prolidase with promiscuous organophosphorus hydrolase activity
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / prolidase / promiscuous phosphotriesterase
Function / homology
Function and homology information


phosphoric triester hydrolase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / metalloexopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Xaa-Pro dipeptidase / : / Xaa-Pro dipeptidase, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily ...Xaa-Pro dipeptidase / : / Xaa-Pro dipeptidase, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesPseudoalteromonas lipolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsJian, Y.
CitationJournal: Biotechnol.Bioeng. / Year: 2020
Title: Repurposing a bacterial prolidase for organophosphorus hydrolysis: Reshaped catalytic cavity switches substrate selectivity.
Authors: Yang, J. / Xiao, Y.Z. / Li, R. / Liu, Y. / Long, L.J.
History
DepositionAug 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Xaa-Pro dipeptidase
B: Xaa-Pro dipeptidase
C: Xaa-Pro dipeptidase
D: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,28415
Polymers206,5574
Non-polymers72811
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-152 kcal/mol
Surface area70720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.854, 178.854, 371.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Xaa-Pro dipeptidase / X-Pro dipeptidase / Imidodipeptidase / Proline dipeptidase / Prolidase


Mass: 51639.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas lipolytica (bacteria)
Gene: pepQ, SAMN04487854_12236 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I7CHQ2, Xaa-Pro dipeptidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M Ammonium sulfate, 5% PEG400, 100 mM MES pH6.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 70044 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2 / Num. unique obs: 6932 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZWO

4zwo


Resolution: 2.61→44.53 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 18.959 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 0.757 / ESU R Free: 0.345 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3493 5 %RANDOM
Rwork0.226 ---
obs-66253 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 72.136 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å21.07 Å2-0 Å2
2--2.14 Å2-0 Å2
3----6.93 Å2
Refinement stepCycle: 1 / Resolution: 2.61→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14256 0 23 86 14365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01414676
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712764
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.65119930
X-RAY DIFFRACTIONr_angle_other_deg0.7491.63129900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80451752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82423.099852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.344152376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5951572
X-RAY DIFFRACTIONr_chiral_restr0.0460.21839
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216648
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022888
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6097.3477020
X-RAY DIFFRACTIONr_mcbond_other3.6067.3467019
X-RAY DIFFRACTIONr_mcangle_it5.70411.0158768
X-RAY DIFFRACTIONr_mcangle_other5.70411.0168769
X-RAY DIFFRACTIONr_scbond_it3.2897.6027656
X-RAY DIFFRACTIONr_scbond_other3.2787.5977641
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.37911.31511143
X-RAY DIFFRACTIONr_long_range_B_refined8.26884.69116096
X-RAY DIFFRACTIONr_long_range_B_other8.26784.69216090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.606→2.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 238 -
Rwork0.37 4874 -
obs--99.38 %

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