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- PDB-5yhp: Proline iminopeptidase from Psychrophilic yeast glaciozyma antarctica -

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Basic information

Entry
Database: PDB / ID: 5yhp
TitleProline iminopeptidase from Psychrophilic yeast glaciozyma antarctica
ComponentsCold active proline iminopeptidase
KeywordsHYDROLASE / COLD ACTIVE ENZYME / PROTEASE / AMINOPEPTIDASE / SERINE PEPTIDASE
Function / homology
Function and homology information


prolyl aminopeptidase / aminopeptidase activity / cytoplasm
Similarity search - Function
Proline iminopeptidase / Peptidase S33 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Proline iminopeptidase
Similarity search - Component
Biological speciesGlaciozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsRodzli, N.A. / Kamaruddin, S. / Jonet, A. / Seman, W.M.K.W. / Tab, M.M. / Minor, N. / Jaafar, N.R. / Mahadi, N.M. / Murad, A.M.A. / Bakar, F.D.A. / Illias, R.M.D.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
MINISTRY OF SCIENCE, TECHNOLOGY AND INNOVATION MALAYSIA02-05-20-SF0007 Malaysia
CitationJournal: To Be Published
Title: Proline iminopeptidase from Psychrophilic yeast glaciozyma antarctica
Authors: Kamaruddin, S. / Rodzli, N.A. / Jonet, A. / Seman, W.M.K.W. / Tab, M.M. / Minor, N. / Jaafar, N.R. / Mahadi, N.M. / Murad, A.M.A. / Bakar, F.D.A.
History
DepositionSep 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cold active proline iminopeptidase
B: Cold active proline iminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7085
Polymers79,1412
Non-polymers5673
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-14 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.388, 82.269, 171.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 2:319 )
21chain B and (resseq 2:319 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 2:319 )
211chain 'B' and (resseq 2:319 )

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Components

#1: Protein Cold active proline iminopeptidase


Mass: 39570.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glaciozyma antarctica (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4A311*PLUS, prolyl aminopeptidase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277.1 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.2M Ammonium acetate, 0.1M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.393→27.694 Å / Num. obs: 28758 / % possible obs: 90.81 % / Redundancy: 2.4 % / Biso Wilson estimate: 64.04 Å2 / Net I/σ(I): 6.12

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1azw

1azw


Resolution: 2.393→27.694 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.95
RfactorNum. reflection% reflection
Rfree0.2151 1997 6.95 %
Rwork0.1856 --
obs0.1877 28744 90.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.393→27.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4998 0 39 140 5177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085174
X-RAY DIFFRACTIONf_angle_d1.1287029
X-RAY DIFFRACTIONf_dihedral_angle_d15.6221910
X-RAY DIFFRACTIONf_chiral_restr0.09741
X-RAY DIFFRACTIONf_plane_restr0.005918
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2495X-RAY DIFFRACTIONPOSITIONAL
12B2495X-RAY DIFFRACTIONPOSITIONAL0.069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.393-2.45280.31381090.26391472X-RAY DIFFRACTION72
2.4528-2.51910.35351200.27331600X-RAY DIFFRACTION76
2.5191-2.59310.30581230.2741668X-RAY DIFFRACTION81
2.5931-2.67680.31261300.25621734X-RAY DIFFRACTION83
2.6768-2.77240.34841330.26321787X-RAY DIFFRACTION86
2.7724-2.88330.31011380.25861837X-RAY DIFFRACTION89
2.8833-3.01430.30281450.26471944X-RAY DIFFRACTION93
3.0143-3.1730.2841510.24482025X-RAY DIFFRACTION97
3.173-3.37150.29461540.2332063X-RAY DIFFRACTION99
3.3715-3.63130.24111570.21372096X-RAY DIFFRACTION99
3.6313-3.99580.21471580.17352111X-RAY DIFFRACTION99
3.9958-4.57170.18911570.15042098X-RAY DIFFRACTION99
4.5717-5.75140.15511580.14212129X-RAY DIFFRACTION99
5.7514-27.69580.14991640.14752183X-RAY DIFFRACTION96
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)
10.11110.1194-0.10150.79550.19720.22930.0148-0.20120.27850.11780.0635-0.1479-0.07940.0260.00020.6326-0.01780.06220.678-0.0460.730431.2643-21.5668-21.8631
20.3918-0.0750.03310.41420.11070.03670.1083-0.10.1381-0.0017-0.03140.0093-0.04-0.0008-00.6121-0.00370.02410.63290.01470.612915.9191-36.1223-26.044
30.1575-0.0423-0.07810.4876-0.20560.13430.14260.06140.23440.06060.1397-0.0988-0.27640.09190.00010.68870.018500.6658-0.02770.641219.5598-34.0045-26.012
40.2511-0.3061-0.00860.3985-0.06710.2519-0.05480.07190.07280.0005-0.0233-0.1153-0.03770.047900.61170.02640.04710.64350.05710.643934.3313-42.6411-25.0424
50.5922-0.0788-0.10350.3195-0.14180.097-0.133-0.2209-0.1918-0.0390.1176-0.11330.08880.2014-0.00010.67820.02520.03820.67750.06260.656516.2562-82.323-11.3297
60.48040.4938-0.39180.7598-0.10690.5938-0.05350.0148-0.0214-0.05610.01730.04470.06530.0347-00.58130.0240.03220.57920.01680.582112.8991-68.5525-22.5508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 255 )
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 319 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 66 )
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 319 )

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