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- PDB-3s2n: Crystal structure of dipeptidase from Streptomyces coelicolor com... -

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Basic information

Entry
Database: PDB / ID: 3s2n
TitleCrystal structure of dipeptidase from Streptomyces coelicolor complexed with phosphinate pseudodipeptide L-Tyr-D-Asp
Componentsdipeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / (beta-alpha)8 barrel / dipeptidase / phosphinate pseudodipeptide L-Tyr-D-Asp / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


metallodipeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-P4D / Dipeptidase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of dipeptidase from Streptomyces coelicolor complexed with phosphinate pseudodipeptide L-Tyr-D-Asp
Authors: Fedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Almo, S.C.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,20311
Polymers43,3061
Non-polymers89710
Water11,422634
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.922, 96.922, 104.711
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

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Components

#1: Protein dipeptidase


Mass: 43306.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO3058, SCBAC19G2.13c / Production host: Escherichia coli (E. coli) / References: UniProt: Q93J45
#2: Chemical ChemComp-P4D / (2R)-2-{[(S)-[(1R)-1-amino-2-(4-hydroxyphenyl)ethyl](hydroxy)phosphoryl]methyl}butanedioic acid / L-TYR-D-ASP PHOSPHINATE PSEUDODIPEPTIDE


Type: peptide-like / Mass: 331.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18NO7P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% Polyacrylic acid, 0.1M hepes, 0.02M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 21, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.4→32.228 Å / Num. all: 108779 / Num. obs: 108779 / % possible obs: 97.15 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K5X

3k5x


Resolution: 1.4→32.228 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 14.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1639 5431 4.99 %RANDOM
Rwork0.1546 ---
all0.155 108779 --
obs0.155 108779 97.15 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.308 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2892 Å20 Å20 Å2
2---1.2892 Å20 Å2
3---2.5785 Å2
Refinement stepCycle: LAST / Resolution: 1.4→32.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 52 634 3676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063131
X-RAY DIFFRACTIONf_angle_d1.1154251
X-RAY DIFFRACTIONf_dihedral_angle_d11.3511150
X-RAY DIFFRACTIONf_chiral_restr0.073472
X-RAY DIFFRACTIONf_plane_restr0.005569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3995-1.41540.29481280.3142541X-RAY DIFFRACTION72
1.4154-1.43210.29371620.28312848X-RAY DIFFRACTION81
1.4321-1.44950.28141500.26073018X-RAY DIFFRACTION86
1.4495-1.46790.24581510.21953149X-RAY DIFFRACTION89
1.4679-1.48720.20141590.20073300X-RAY DIFFRACTION93
1.4872-1.50760.19551980.18663347X-RAY DIFFRACTION96
1.5076-1.52910.17381900.16763410X-RAY DIFFRACTION98
1.5291-1.55190.1772010.15213469X-RAY DIFFRACTION99
1.5519-1.57620.14521850.1493507X-RAY DIFFRACTION100
1.5762-1.6020.17521730.14213548X-RAY DIFFRACTION100
1.602-1.62960.16081820.14153536X-RAY DIFFRACTION100
1.6296-1.65930.14171630.14213573X-RAY DIFFRACTION100
1.6593-1.69120.17441910.14163496X-RAY DIFFRACTION100
1.6912-1.72570.14441720.13493526X-RAY DIFFRACTION100
1.7257-1.76320.14451840.13733572X-RAY DIFFRACTION100
1.7632-1.80420.15791940.13353504X-RAY DIFFRACTION100
1.8042-1.84930.15761860.13553536X-RAY DIFFRACTION100
1.8493-1.89930.15851900.14013522X-RAY DIFFRACTION100
1.8993-1.95520.13981800.1413548X-RAY DIFFRACTION100
1.9552-2.01830.16821970.15083529X-RAY DIFFRACTION100
2.0183-2.09050.1581890.1483511X-RAY DIFFRACTION100
2.0905-2.17410.15571840.14913562X-RAY DIFFRACTION100
2.1741-2.27310.14851620.14893591X-RAY DIFFRACTION100
2.2731-2.39290.15131900.14463550X-RAY DIFFRACTION100
2.3929-2.54270.16391940.15073560X-RAY DIFFRACTION100
2.5427-2.7390.16231900.14993583X-RAY DIFFRACTION100
2.739-3.01440.15441940.15773565X-RAY DIFFRACTION100
3.0144-3.45020.16921930.15163604X-RAY DIFFRACTION100
3.4502-4.34520.13862020.1423626X-RAY DIFFRACTION100
4.3452-32.23680.18851970.17623717X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -25.1312 Å / Origin y: 22.1091 Å / Origin z: -15.9622 Å
111213212223313233
T0.0958 Å20.0031 Å20.0092 Å2-0.0909 Å20.0002 Å2--0.0964 Å2
L0.1094 °2-0.0223 °2-0.0584 °2-0.2443 °20.0279 °2--0.2944 °2
S0.0108 Å °-0.0073 Å °0.0205 Å °0.0288 Å °-0.0055 Å °-0.004 Å °-0.0175 Å °-0.0126 Å °-0.0071 Å °
Refinement TLS groupSelection details: chain A

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