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- PDB-5xev: Crystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus... -

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Basic information

Entry
Database: PDB / ID: 5xev
TitleCrystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus radiodurans
ComponentsXaa-Pro dipeptidase,Peptidase-related protein
KeywordsHYDROLASE / Xaa-Pro dipeptidase / prolidase / M28B peptidase / Deinococcus radiodurans
Function / homology: / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / metal ion binding / ACETATE ION / PHOSPHATE ION / Peptidase-related protein
Function and homology information
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAre, V.N. / Kumar, A. / Ghosh, B. / Makde, R.D.
CitationJournal: Proteins / Year: 2017
Title: Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases.
Authors: Are, V.N. / Jamdar, S.N. / Ghosh, B. / Goyal, V.D. / Kumar, A. / Neema, S. / Gadre, R. / Makde, R.D.
History
DepositionApr 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xaa-Pro dipeptidase,Peptidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6917
Polymers45,3081
Non-polymers3826
Water7,512417
1
A: Xaa-Pro dipeptidase,Peptidase-related protein
hetero molecules

A: Xaa-Pro dipeptidase,Peptidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,38114
Polymers90,6172
Non-polymers76512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3670 Å2
ΔGint-29 kcal/mol
Surface area31360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.670, 91.879, 53.849
Angle α, β, γ (deg.)90.00, 98.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

21A-866-

HOH

31A-882-

HOH

41A-969-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Xaa-Pro dipeptidase,Peptidase-related protein


Mass: 45308.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Plasmid: pST50STRHIS
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0478 / Details (production host): T7 based expression plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9RX37, Xaa-Pro dipeptidase

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Non-polymers , 6 types, 423 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThis protein corresponds to database(UniParc:UPI0002D66B97,GenBank:ANC72273).

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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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 4.8
Details: 40 mM KH2PO4, 10mM ammonium citrate, pH 4.8, 3 mM phenylalanine, 1 mM MnCl2, 10 mM ZnCl2, 16% PEG8000, 20% Glycerol
PH range: 4.5-5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 29, 2016 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.4→45.94 Å / Num. obs: 85429 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Net I/σ(I): 15.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4196 / CC1/2: 0.757 / Rpim(I) all: 0.331 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152)refinement
AUTOMARdata collection
XDSdata processing
Aimlessdata scaling
AutoSolphasing
Cootmodel building
RESOLVEmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→31.955 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.77
RfactorNum. reflection% reflectionSelection details
Rfree0.1639 4130 4.84 %random
Rwork0.1464 ---
obs0.1473 85413 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→31.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 16 417 3571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073270
X-RAY DIFFRACTIONf_angle_d0.9184468
X-RAY DIFFRACTIONf_dihedral_angle_d14.1831154
X-RAY DIFFRACTIONf_chiral_restr0.072477
X-RAY DIFFRACTIONf_plane_restr0.006602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.2941350.24212704X-RAY DIFFRACTION99
1.4159-1.43260.27391430.22632634X-RAY DIFFRACTION100
1.4326-1.450.2351350.20632716X-RAY DIFFRACTION100
1.45-1.46840.20641470.20012680X-RAY DIFFRACTION100
1.4684-1.48770.21911350.18862683X-RAY DIFFRACTION100
1.4877-1.50810.19081290.18412733X-RAY DIFFRACTION100
1.5081-1.52960.19391350.17662707X-RAY DIFFRACTION100
1.5296-1.55250.19891390.17652692X-RAY DIFFRACTION100
1.5525-1.57670.17391260.17242730X-RAY DIFFRACTION100
1.5767-1.60260.19561370.16532685X-RAY DIFFRACTION100
1.6026-1.63020.18961400.16682692X-RAY DIFFRACTION100
1.6302-1.65990.17591500.15942705X-RAY DIFFRACTION100
1.6599-1.69180.17291610.14892707X-RAY DIFFRACTION100
1.6918-1.72630.16831350.15212717X-RAY DIFFRACTION100
1.7263-1.76380.16861560.14962653X-RAY DIFFRACTION100
1.7638-1.80490.14581340.14522732X-RAY DIFFRACTION100
1.8049-1.850.16621280.14352714X-RAY DIFFRACTION100
1.85-1.90.17131300.14632715X-RAY DIFFRACTION100
1.9-1.95590.15881320.14382728X-RAY DIFFRACTION100
1.9559-2.0190.14831210.14562710X-RAY DIFFRACTION100
2.019-2.09120.19631240.14252747X-RAY DIFFRACTION100
2.0912-2.17490.16681350.13422706X-RAY DIFFRACTION100
2.1749-2.27390.15421360.13482722X-RAY DIFFRACTION100
2.2739-2.39370.14511440.12962729X-RAY DIFFRACTION100
2.3937-2.54360.14921440.13562697X-RAY DIFFRACTION100
2.5436-2.73990.14251510.1362694X-RAY DIFFRACTION100
2.7399-3.01550.15811280.14262723X-RAY DIFFRACTION100
3.0155-3.45140.15941420.14372723X-RAY DIFFRACTION99
3.4514-4.34660.15211290.13312739X-RAY DIFFRACTION100
4.3466-31.96310.14721490.13972766X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.9916 Å / Origin y: -21.9256 Å / Origin z: 1.6981 Å
111213212223313233
T0.1305 Å2-0.0015 Å2-0.0137 Å2-0.1087 Å20.0008 Å2--0.127 Å2
L0.6741 °20.3797 °2-0.3392 °2-0.2732 °2-0.2199 °2--0.4129 °2
S0.0048 Å °-0.014 Å °-0.0123 Å °-0.0044 Å °-0.0079 Å °0.0044 Å °0.0286 Å °-0.0223 Å °0.011 Å °
Refinement TLS groupSelection details: all

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