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- PDB-2d5l: Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porph... -

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Basic information

Entry
Database: PDB / ID: 2d5l
TitleCrystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
Componentsdipeptidyl aminopeptidase IV, putative
KeywordsHYDROLASE / peptidase family S9 / serine peptidase / prolyl oligopeptidase family
Function / homology
Function and homology information


Xaa-Xaa-Pro tripeptidyl-peptidase / dipeptidyl-peptidase activity / aminopeptidase activity / serine-type peptidase activity / proteolysis
Similarity search - Function
Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Prolyl tripeptidyl peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsNakajima, Y. / Ito, K. / Xu, Y. / Yamada, N. / Onohara, Y. / Yoshimoto, T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure and Mechanism of Tripeptidyl Activity of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
Authors: Ito, K. / Nakajima, Y. / Xu, Y. / Yamada, N. / Onohara, Y. / Ito, T. / Matsubara, F. / Kabashima, T. / Nakayama, K. / Yoshimoto, T.
History
DepositionNov 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dipeptidyl aminopeptidase IV, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7012
Polymers79,6051
Non-polymers961
Water7,548419
1
A: dipeptidyl aminopeptidase IV, putative
hetero molecules

A: dipeptidyl aminopeptidase IV, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,4024
Polymers159,2102
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_556-x,-x+y,-z+11
Unit cell
Length a, b, c (Å)149.394, 149.394, 159.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein dipeptidyl aminopeptidase IV, putative / prolyl tripeptidyl aminopeptidase


Mass: 79604.781 Da / Num. of mol.: 1 / Fragment: residues 39-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG1361 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q7MUW6, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.1M potassium sodium tartrate, 0.2M lithium sulfate, 0.1M CHES buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
ROTATING ANODERIGAKU MICROMAX-00721.5418
ROTATING ANODERIGAKU MICROMAX-00731.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 9, 2004
RIGAKU RAXIS IV2IMAGE PLATEOct 27, 2004
RIGAKU RAXIS IV3IMAGE PLATEOct 28, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2confocal mirrorSINGLE WAVELENGTHMx-ray1
3confocal mirrorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.54181
ReflectionResolution: 2.1→50 Å / Num. all: 61466 / Num. obs: 61466 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 85
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 15.3 / Num. unique all: 6027 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3106 -random
Rwork0.203 ---
all-61208 --
obs-61208 99.5 %-
Displacement parametersBiso mean: 37.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-6 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 5 419 5704
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.74

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