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- PDB-4r0k: Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314)... -

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Basic information

Entry
Database: PDB / ID: 4r0k
TitleCrystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from Bacteroides thetaiotaomicron VPI-5482 at 1.75 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


Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / SH3 Domains / Papain-like cysteine peptidase superfamily / SH3 type barrels. ...Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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)71,89613
Polymers71,2592
Non-polymers63611
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-45 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.030, 50.570, 107.870
Angle α, β, γ (deg.)90.000, 93.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dipeptidyl-peptidase VI


Mass: 35629.645 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.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15.00% Glycerol, 8.500% iso-Propanol, 17.00% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2011
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→45.767 Å / Num. obs: 66413 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.271 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.810.4432.115017631793.7
1.81-1.890.3272.616797718192.8
1.89-1.970.223.814539609692.7
1.97-2.070.2045.118758647895.3
2.07-2.20.147720140674894.4
2.2-2.370.1119.119124653192.1
2.37-2.610.0911.120719684495.3
2.61-2.990.06514.819631661092
2.99-3.760.04321.820642683096
3.760.03227.619880677892

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.767 Å / Cor.coef. Fo:Fc: 0.9513 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.3 / 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. ETHYLENE GLYCOL (EDO), 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 291 WAS MONO-OXIDIZED BASED ON THE ELECTRON DENSITY. CYSTEINE 203 WAS MODELED AS S-ACETONYLCYSTEINE BASED ON DENSITY. 6. THIS CRYSTAL IS IDENTICAL TO THAT OF PDB ENTRY 3PVQ. IT WAS OBTAINED IN A DIFFERENT CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 3280 4.94 %RANDOM
Rwork0.1536 ---
obs0.1548 66391 93.59 %-
Displacement parametersBiso max: 113.66 Å2 / Biso mean: 31.6931 Å2 / Biso min: 13.08 Å2
Baniso -1Baniso -2Baniso -3
1-7.9772 Å20 Å21.716 Å2
2---10.255 Å20 Å2
3---2.2778 Å2
Refine analyzeLuzzati coordinate error obs: 0.201 Å
Refinement stepCycle: LAST / Resolution: 1.75→45.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4883 0 36 568 5487
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3036SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes119HARMONIC2
X-RAY DIFFRACTIONt_gen_planes801HARMONIC5
X-RAY DIFFRACTIONt_it5228HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion666SEMIHARMONIC5
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_contact6401SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5228HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7106HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion4.21
X-RAY DIFFRACTIONt_other_torsion1.76
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2481 236 4.88 %
Rwork0.2104 4605 -
all0.2122 4841 -
obs--93.59 %
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)
11.6304-0.0128-0.08210.31020.03971.12950.01890.2860.08120.0133-0.03060.0289-0.034-0.29520.0117-0.12210.0059-0.0060.02680.0121-0.110139.110630.117982.5909
21.2511-0.02230.01860.2584-0.05950.9780.00550.19860.0636-0.0111-0.0021-0.0216-0.00090.1114-0.0034-0.07160.0044-0.0054-0.01370.0159-0.070666.643429.708980.8301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|26 - 328}A26 - 328
2X-RAY DIFFRACTION2{B|25 - 328}B25 - 328

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