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- PDB-5giq: Xaa-Pro peptidase from Deinococcus radiodurans, Zinc bound -

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Basic information

Entry
Database: PDB / ID: 5giq
TitleXaa-Pro peptidase from Deinococcus radiodurans, Zinc bound
ComponentsProline dipeptidase
KeywordsHYDROLASE / Xaa-Pro peptidase / M24B fold / proline-specific
Function / homology
Function and homology information


metalloexopeptidase activity / aminopeptidase activity / metal ion binding
Similarity search - Function
: / Creatinase, N-terminal / Creatinase/Prolidase 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 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase ...: / Creatinase, N-terminal / Creatinase/Prolidase 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 / Peptidase M24, methionine aminopeptidase / 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
PHOSPHATE ION / Proline dipeptidase
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAre, V.N. / Singh, R. / Kumar, A. / Ghosh, B. / Jamdar, S.N. / Makde, R.D.
CitationJournal: Proteins / Year: 2018
Title: Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases.
Authors: Are, V.N. / Kumar, A. / Goyal, V.D. / Gotad, S.S. / Ghosh, B. / Gadre, R. / Jamdar, S.N. / Makde, R.D.
History
DepositionJun 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Proline dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3734
Polymers37,1471
Non-polymers2263
Water5,603311
1
A: Proline dipeptidase
hetero molecules

A: Proline dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7458
Polymers74,2932
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3130 Å2
ΔGint-179 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.007, 60.007, 202.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Proline dipeptidase


Mass: 37146.742 Da / Num. of mol.: 1 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / Gene: DR_1246 / Plasmid: pST50STR / Details (production host): pET3a , T7 expression system / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RUY4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.46 Å3/Da / Density % sol: 49.96 % / Description: Octohedron like
Crystal growTemperature: 294 K / Method: microbatch / pH: 4.6
Details: 0.1M Phospho-Citrate pH 4.54, 0.2M NaCl, 22% PEG 8000

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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: Jun 21, 2016 / Details: Mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.8→39.14 Å / Num. obs: 34916 / % possible obs: 98.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3 % / Rmerge(I) obs: 0.335 / % possible all: 81.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata processing
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CDV

5cdv


Resolution: 1.8→39.14 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.65
RfactorNum. reflection% reflection
Rfree0.1953 1764 5.07 %
Rwork0.1645 --
obs0.1661 34815 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 7 311 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112639
X-RAY DIFFRACTIONf_angle_d1.0843585
X-RAY DIFFRACTIONf_dihedral_angle_d14.2061590
X-RAY DIFFRACTIONf_chiral_restr0.071414
X-RAY DIFFRACTIONf_plane_restr0.007475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.26091150.24182105X-RAY DIFFRACTION83
1.8487-1.90310.23061410.21272361X-RAY DIFFRACTION94
1.9031-1.96450.21591270.1912544X-RAY DIFFRACTION100
1.9645-2.03470.21341190.17152548X-RAY DIFFRACTION100
2.0347-2.11620.19741400.16552548X-RAY DIFFRACTION100
2.1162-2.21250.21881300.15852543X-RAY DIFFRACTION100
2.2125-2.32910.19111280.15732569X-RAY DIFFRACTION100
2.3291-2.4750.21721430.15812560X-RAY DIFFRACTION100
2.475-2.66610.20051410.16472583X-RAY DIFFRACTION100
2.6661-2.93430.18281490.16512595X-RAY DIFFRACTION100
2.9343-3.35870.20511460.16312613X-RAY DIFFRACTION100
3.3587-4.23080.18241440.14962657X-RAY DIFFRACTION100
4.2308-39.140.16551410.16162825X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.1504 Å / Origin y: -20.8762 Å / Origin z: -12.4126 Å
111213212223313233
T0.1414 Å20.0306 Å2-0.0002 Å2-0.1135 Å20.0008 Å2--0.1292 Å2
L0.6557 °20.2381 °20.4 °2-0.3712 °20.1493 °2--0.9437 °2
S0.0425 Å °0.0186 Å °-0.0151 Å °-0.0066 Å °-0.0072 Å °-0.0177 Å °0.0364 Å °-0.005 Å °-0.0391 Å °
Refinement TLS groupSelection details: all

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