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- PDB-5cdl: Proline dipeptidase from Deinococcus radiodurans (selenomethionin... -

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Basic information

Entry
Database: PDB / ID: 5cdl
TitleProline dipeptidase from Deinococcus radiodurans (selenomethionine derivative)
ComponentsProline dipeptidase
KeywordsHYDROLASE / Xaa-pro dipeptidase / prolidase / Deinococcus radiodurans
Function / homology
Function and homology information


metalloaminopeptidase activity / transition metal ion binding / proteolysis
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 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.
CitationJournal: To Be Published
Title: Proline dipeptidase from Deinococcus radiodurans (selenomethionine derivative)
Authors: Kumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.
History
DepositionJul 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_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)37,7685
Polymers37,4281
Non-polymers3404
Water5,405300
1
A: Proline dipeptidase
hetero molecules

A: Proline dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,53610
Polymers74,8562
Non-polymers6808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3970 Å2
ΔGint-67 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.632, 60.632, 202.824
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: 37428.105 Da / Num. of mol.: 1 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_1246 / Plasmid: pST50Tr / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9RUY4
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5 / Details: 0.1M HEPES pH 7.5, 0.8M NaH2PO4, 0.8M KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97885 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 13, 2013
RadiationMonochromator: double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 1.8→45.14 Å / Num. obs: 35744 / % possible obs: 98.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 1.9 / % possible all: 85.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
REFMACrefinement
Cootmodel building
RESOLVEphasing
SOLVEphasing
Aimlessdata scaling
XDSdata processing
MAR345dtbdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.8→45.139 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1785 5 %Random
Rwork0.1774 ---
obs0.1786 35666 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 16 300 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072656
X-RAY DIFFRACTIONf_angle_d1.0843613
X-RAY DIFFRACTIONf_dihedral_angle_d11.839972
X-RAY DIFFRACTIONf_chiral_restr0.044416
X-RAY DIFFRACTIONf_plane_restr0.005478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7998-1.84850.28141170.27032239X-RAY DIFFRACTION86
1.8485-1.90290.25261240.23812477X-RAY DIFFRACTION95
1.9029-1.96430.21611280.21912588X-RAY DIFFRACTION100
1.9643-2.03450.23031390.19472592X-RAY DIFFRACTION100
2.0345-2.11590.19311400.18542587X-RAY DIFFRACTION100
2.1159-2.21220.22711140.16992622X-RAY DIFFRACTION100
2.2122-2.32890.19911440.17352629X-RAY DIFFRACTION100
2.3289-2.47480.1981510.18182584X-RAY DIFFRACTION100
2.4748-2.66580.21571600.18622625X-RAY DIFFRACTION100
2.6658-2.9340.21871510.18942638X-RAY DIFFRACTION100
2.934-3.35850.20651350.17622689X-RAY DIFFRACTION100
3.3585-4.23090.16741360.14872727X-RAY DIFFRACTION100
4.2309-45.1530.17241460.15882884X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.17880.63450.82151.34170.62212.09910.09060.1162-0.14330.04260.029-0.10380.17560.0791-0.09720.09260.0233-0.02040.1106-0.00680.119635.052713.3448100.841
23.3873-1.1408-0.38881.41870.32711.3923-0.04080.10170.10740.07130.03040.0299-0.0005-0.22270.01690.10490.0033-0.00430.13020.01790.08021.97643.246290.367
30.7290.5765-0.4740.505-0.07822.05670.00920.14950.1423-0.05980.12020.1057-0.1748-0.3338-0.08470.10810.03950.00130.17180.02760.13778.06579.850475.6222
41.87140.6875-0.19791.0251-0.47111.7613-0.0040.0780.06870.01740.05530.0057-0.1548-0.1014-0.0240.11470.02180.00270.1301-0.01630.094214.71587.799978.9959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid 206 through 285 )
4X-RAY DIFFRACTION4chain 'A' and (resid 286 through 349 )

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