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- PDB-6ah7: D45W/H226G mutant of marine bacterial prolidase -

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Basic information

Entry
Database: PDB / ID: 6ah7
TitleD45W/H226G mutant of marine bacterial prolidase
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / paraoxonase
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, N-terminal domain / Xaa-Pro dipeptidase / 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, N-terminal domain / Xaa-Pro dipeptidase / 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: 2.38 Å
AuthorsJian, Y. / Yunzhu, X. / Lijuan, L.
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 25, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Sep 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_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Nov 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

Downloads & links

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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)207,07514
Polymers206,5174
Non-polymers55910
Water10,178565
1
A: Xaa-Pro dipeptidase
B: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5978
Polymers103,2582
Non-polymers3396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-72 kcal/mol
Surface area35900 Å2
MethodPISA
2
C: Xaa-Pro dipeptidase
D: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4786
Polymers103,2582
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-56 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.632, 183.632, 371.306
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: 51629.164 Da / Num. of mol.: 4 / Mutation: D45W/H226G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas lipolytica (bacteria)
Gene: pepQ, SAMN04487854_12236 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.92 Å3/Da / Density % sol: 58.7 %
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: BL17B1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.38→67.29 Å / Num. obs: 94764 / % possible obs: 97.8 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 12.5
Reflection shellResolution: 2.38→2.5 Å / Rmerge(I) obs: 1.498 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 14041 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zwo

4zwo


Resolution: 2.38→67.29 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.2693 4417 -
Rwork0.2332 --
obs-91647 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.38→67.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14256 0 14 565 14835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414824
X-RAY DIFFRACTIONf_angle_d0.64120150
X-RAY DIFFRACTIONf_dihedral_angle_d5.68912088
X-RAY DIFFRACTIONf_chiral_restr0.0452105
X-RAY DIFFRACTIONf_plane_restr0.0042663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3759-2.40290.34681520.30073051X-RAY DIFFRACTION100
2.4029-2.43120.28311610.27853062X-RAY DIFFRACTION100
2.4312-2.46080.34241450.26523034X-RAY DIFFRACTION100
2.4608-2.4920.30041410.26293075X-RAY DIFFRACTION100
2.492-2.52480.2651430.25673031X-RAY DIFFRACTION100
2.5248-2.55940.31291660.26013052X-RAY DIFFRACTION100
2.5594-2.59590.37581550.27443044X-RAY DIFFRACTION100
2.5959-2.63470.28261370.28542714X-RAY DIFFRACTION95
2.6347-2.67580.5237680.51581787X-RAY DIFFRACTION69
2.6758-2.71970.42131500.35132663X-RAY DIFFRACTION88
2.7197-2.76660.30851520.26233054X-RAY DIFFRACTION100
2.7666-2.81690.2641420.24653057X-RAY DIFFRACTION100
2.8169-2.87110.29361420.24193066X-RAY DIFFRACTION100
2.8711-2.92970.2771480.23783034X-RAY DIFFRACTION100
2.9297-2.99340.26951580.23153064X-RAY DIFFRACTION100
2.9934-3.0630.2741570.24893058X-RAY DIFFRACTION100
3.063-3.13960.32471780.25433040X-RAY DIFFRACTION100
3.1396-3.22450.34081480.2483051X-RAY DIFFRACTION100
3.2245-3.31940.27941620.25183060X-RAY DIFFRACTION100
3.3194-3.42650.4151200.28192783X-RAY DIFFRACTION91
3.4265-3.5490.3651550.31062845X-RAY DIFFRACTION92
3.549-3.69110.3116640.24471161X-RAY DIFFRACTION38
3.6911-3.85910.28131460.22882897X-RAY DIFFRACTION94
3.8591-4.06250.29911370.27292877X-RAY DIFFRACTION93
4.0625-4.3170.21971530.1823070X-RAY DIFFRACTION99
4.317-4.65020.19581540.16523087X-RAY DIFFRACTION99
4.6502-5.11810.19111560.16683089X-RAY DIFFRACTION100
5.1181-5.85830.22321640.1853099X-RAY DIFFRACTION100
5.8583-7.37940.22021790.21143121X-RAY DIFFRACTION100
7.3794-67.31360.1991840.18173204X-RAY DIFFRACTION99

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