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- PDB-2ecf: Crystal Structure of Dipeptidyl Aminopeptidase IV from Stenotroph... -

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Basic information

Entry
Database: PDB / ID: 2ecf
TitleCrystal Structure of Dipeptidyl Aminopeptidase IV from Stenotrophomonas maltophilia
ComponentsDipeptidyl peptidase IV
KeywordsHYDROLASE / prolyl oligopeptidase family / peptidase family S9 / dipeptidyl peptidase IV
Function / homology
Function and homology information


serine-type peptidase activity
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 ...: / 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
Dipeptidyl peptidase IV
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.8 Å
AuthorsNakajima, Y. / Ito, K. / Yoshimoto, T.
CitationJournal: J.Bacteriol. / Year: 2008
Title: Dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia exhibits activity against a substrate containing a 4-hydroxyproline residue
Authors: Nakajima, Y. / Ito, K. / Toshima, T. / Egawa, T. / Zheng, H. / Oyama, H. / Wu, Y.-F. / Takahashi, E. / Kyono, K. / Yoshimoto, T.
History
DepositionFeb 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptidyl peptidase IV


Theoretical massNumber of molelcules
Total (without water)82,1801
Polymers82,1801
Non-polymers00
Water1,18966
1
A: Dipeptidyl peptidase IV

A: Dipeptidyl peptidase IV


Theoretical massNumber of molelcules
Total (without water)164,3612
Polymers164,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area2650 Å2
ΔGint-15 kcal/mol
Surface area54350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.877, 105.877, 161.895
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 Dipeptidyl peptidase IV / / Dipeptidyl aminopeptidase IV


Mass: 82180.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P95782, dipeptidyl-peptidase IV
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 12% PEG 6000, 0.2M magnesium chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
32981
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
ROTATING ANODERIGAKU RU20021.5418
ROTATING ANODERIGAKU RU20031.5418
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEMar 7, 2003monochrometor
RIGAKU RAXIS IV2IMAGE PLATEJul 3, 2003Osmic mirror
RIGAKU RAXIS IV3IMAGE PLATEJul 3, 2003monochrometor
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2osmic mirrorSINGLE WAVELENGTHMx-ray1
3graphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→45 Å / Num. obs: 23396 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 56.8 Å2 / Rsym value: 0.077 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3285 / Rsym value: 0.333 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SHARPphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1197 -random
Rwork0.185 ---
all-23282 --
obs-23264 99.9 %-
Displacement parametersBiso mean: 41.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5445 0 0 66 5511
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.811
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.337 120 -
Rwork0.271 --
obs-2151 99.7 %

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