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- PDB-3pvq: Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314)... -

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Basic information

Entry
Database: PDB / ID: 3pvq
TitleCrystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution
ComponentsDipeptidyl-peptidase VI
KeywordsHYDROLASE / CYSTEINE PROTEINASE FOLD / SH3-LIKE BARREL / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


peptidoglycan metabolic process / cysteine-type peptidase activity / endopeptidase activity
Similarity search - Function
Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / SH3 Domains / Papain-like cysteine peptidase superfamily ...Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / SH3 Domains / Papain-like cysteine peptidase superfamily / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Dipeptidyl-peptidase VI
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl-peptidase VI
B: Dipeptidyl-peptidase VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8399
Polymers71,3072
Non-polymers5317
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-41 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.919, 50.295, 107.562
Angle α, β, γ (deg.)90.000, 93.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dipeptidyl-peptidase VI


Mass: 35653.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_1314 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A860
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 22-328) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 22-328) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20.0% Glycerol, 0.04M KH2PO4, 16.0% PEG-8000, No Buffer pH None, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
ReflectionResolution: 2.1→29.159 Å / Num. obs: 40250 / % possible obs: 91 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.817 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 6.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.170.3741.58951639886.6
2.17-2.260.311.910196730488.6
2.26-2.360.2882.19658693689.8
2.36-2.490.2462.510568761390.9
2.49-2.640.1853.39619695891
2.64-2.850.1334.310173738990.7
2.85-3.130.096.29794715991.9
3.13-3.590.05110.39975738491.1
3.59-4.510.03116.49767725092.5
4.510.02718.810321770196.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.159 Å / Cor.coef. Fo:Fc: 0.9453 / Cor.coef. Fo:Fc free: 0.9298 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. GLYCEROL(GOL) AND CHLORIDE (CL) MODELED ARE PRESENT PROTEIN/CRYSTALLIZATION/CRYO BUFFER. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. THE CYSTEINE RESIDUE (203, 291) ARE OXIDIZED BASED ON THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 2019 5.02 %RANDOM
Rwork0.1647 ---
obs0.1664 40234 --
Displacement parametersBiso max: 108.43 Å2 / Biso mean: 30.5614 Å2 / Biso min: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1-6.415 Å20 Å2-0.8607 Å2
2---5.672 Å20 Å2
3----0.743 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 32 448 5266
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2269SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes737HARMONIC5
X-RAY DIFFRACTIONt_it4993HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion627SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5978SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4993HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6774HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion2.63
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2269 120 4.26 %
Rwork0.1979 2699 -
all0.1991 2819 -
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)
12.49390.0333-0.12530.29220.13531.3804-0.00410.16830.13690.0132-0.01280.008-0.0281-0.25020.017-0.15990.0131-0.03030.02850.0051-0.163239.377529.821883.0478
21.87290.0671-0.15520.3447-0.01611.1939-0.00470.10280.0693-0.0099-0.003-0.0107-0.01050.11060.0078-0.11280.003-0.03020.0140.0076-0.127366.731329.187579.9725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|32 - 328 }A32 - 328
2X-RAY DIFFRACTION2{ B|32 - 328 }B32 - 328

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