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- PDB-3k5x: Crystal structure of dipeptidase from Streptomics coelicolor comp... -

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Basic information

Entry
Database: PDB / ID: 3k5x
TitleCrystal structure of dipeptidase from Streptomics coelicolor complexed with phosphinate pseudodipeptide L-Ala-D-Asp at 1.4A resolution.
ComponentsDipeptidase
KeywordsHYDROLASE / dipeptidase from Streptomics coelicolor / the closest bacterial homolog to human renal dipeptidase / phosphinate pseudodipeptide / L-Ala-D-Asp
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
phosphinate pseudodipeptide L-Ala-D-Asp / Dipeptidase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
Model detailsPutative dipeptidase
AuthorsFedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2010
Title: Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .
Authors: Cummings, J.A. / Nguyen, T.T. / Fedorov, A.A. / Kolb, P. / Xu, C. / Fedorov, E.V. / Shoichet, B.K. / Barondeau, D.P. / Almo, S.C. / Raushel, F.M.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)43,6764
Polymers43,3061
Non-polymers3703
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dipeptidase
hetero molecules

A: Dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3528
Polymers86,6122
Non-polymers7406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area3410 Å2
ΔGint-165 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.910, 96.910, 104.190
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-789-

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-P8D / phosphinate pseudodipeptide L-Ala-D-Asp / (2R)-2-{[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]methyl}butanedioic acid


Mass: 239.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14NO6P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.26 Å3/Da / Density % sol: 62.28 %
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: Oct 3, 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→25 Å / Num. all: 106229 / Num. obs: 106229 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ID7

3id7


Resolution: 1.4→24.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1767382.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 5297 5 %RANDOM
Rwork0.193 ---
obs0.193 106229 95.3 %-
all-106229 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.91 Å2 / ksol: 0.366725 e/Å3
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0.51 Å20 Å2
2---1.57 Å20 Å2
3---3.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.4→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 17 417 3413
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it0.741.5
X-RAY DIFFRACTIONc_mcangle_it1.122
X-RAY DIFFRACTIONc_scbond_it1.562
X-RAY DIFFRACTIONc_scangle_it2.222.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.4→1.45 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.382 400 5.1 %
Rwork0.386 7419 -
obs-7419 70.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4P8D_par.txtPAD_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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