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- PDB-5ynl: Structure of Glaciozyma antarctica Arginase Reveals Cold-active A... -

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Entry
Database: PDB / ID: 5ynl
TitleStructure of Glaciozyma antarctica Arginase Reveals Cold-active Adaptation via Increased Flexible Access to the Active Site
ComponentsArginase
KeywordsHYDROLASE / Arginase / Glaciozyma antarctica / enzyme
Function / homology
Function and homology information


: / arginase / arginase activity / urea cycle / manganese ion binding / nucleus / cytosol
Similarity search - Function
Arginase / Ureohydrolase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / Winged helix-like DNA-binding domain superfamily ...Arginase / Ureohydrolase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGlaciozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsQuay, D.H.X. / Yusof, N.Y. / Illias, R.M. / Firdaus-Raih, M. / Abu-Bakar, F.D. / Mahadi, N.M. / Murad, A.M.A.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Ministry of Science, Technology and Innovation (MOSTI, Malaysia)02-05-20-SF0007 Malaysia
CitationJournal: To Be Published
Title: Structure of Glaciozyma antarctica Arginase Reveals Cold-active Adaptation via Increased Flexible Access to the Active Site
Authors: Quay, D.H.X. / Yusof, N.Y. / Illias, R.M. / Abu-Bakar, F.D. / Mahadi, N.M. / Firdaus-Raih, M. / Murad, A.M.A.
History
DepositionOct 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: 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
Revision 2.0Dec 31, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / audit_author / cell / citation / citation_author / diffrn / entity / entity_poly / entity_poly_seq / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_conf / struct_sheet_range
Item: _audit_author.name / _cell.angle_alpha ..._audit_author.name / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _citation.title / _citation_author.name / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_audit_support.funding_organization / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _reflns.pdbx_CC_half / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _software.name / _software.version / _struct.title / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness
Details: The updated model (Deposition ID: D_1300004898) corrects chain breaks and improves model completeness compared to the released entry 5YNL. The new structure includes additional residues, ...Details: The updated model (Deposition ID: D_1300004898) corrects chain breaks and improves model completeness compared to the released entry 5YNL. The new structure includes additional residues, resolves previously disordered regions, and reflects improved geometry and clashscore. This replacement ensures accurate representation of the cold-active arginase structure from Glaciozyma antarctica.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginase


Theoretical massNumber of molelcules
Total (without water)38,7761
Polymers38,7761
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.193, 91.193, 107.779
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Arginase


Mass: 38775.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glaciozyma antarctica (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2R2JFW7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium malonate pH 5, 12 % w/v polyethylene glycol 3,350, 0.1 M TCEP hydrochloride, 10mg/ml purified protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.349→63.7 Å / Num. obs: 13850 / % possible obs: 95 % / Redundancy: 3.7 % / CC1/2: 0.772 / Net I/σ(I): 1.6
Reflection shellResolution: 2.35→2.53 Å / Num. unique obs: 13850 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.126)refinement
HKL-3000data reduction
HKL-3000data scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→28.784 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.893 / SU B: 18.246 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.277 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 689 5 %RANDOM
Rwork0.2206 13092 --
all0.223 ---
obs-13781 98.994 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 57.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.876 Å20.438 Å2-0 Å2
2--0.876 Å20 Å2
3----2.841 Å2
Refinement stepCycle: LAST / Resolution: 2.35→28.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 0 46 2215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122223
X-RAY DIFFRACTIONr_angle_refined_deg2.2851.7993026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4945289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.106513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30810344
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.471089
X-RAY DIFFRACTIONr_chiral_restr0.1760.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021690
X-RAY DIFFRACTIONr_nbd_refined0.1860.2996
X-RAY DIFFRACTIONr_nbtor_refined0.2810.21467
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2110
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0860.25
X-RAY DIFFRACTIONr_mcbond_it2.82.5931168
X-RAY DIFFRACTIONr_mcangle_it4.34.6441453
X-RAY DIFFRACTIONr_scbond_it2.9812.5491055
X-RAY DIFFRACTIONr_scangle_it4.3074.7071573
X-RAY DIFFRACTIONr_lrange_it7.41227.5763261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.35-2.4110.379660.2589450.26510140.9250.96499.70410.215
2.411-2.4760.318480.2119630.21610120.9450.97499.90120.177
2.476-2.5470.335630.2259050.2329690.9350.97299.89680.191
2.547-2.6250.264430.2148890.2179330.9630.97399.89280.178
2.625-2.7110.311450.1888740.1949190.9540.981000.154
2.711-2.8050.257450.2078210.218660.960.9751000.177
2.805-2.910.202580.2148050.2138630.9740.9711000.184
2.91-3.0270.344320.2297990.2348320.9350.96899.87980.199
3.027-3.160.247310.2197450.227760.9610.9731000.201
3.16-3.3120.285490.2196950.2237460.9510.97399.73190.206
3.312-3.4890.243360.2376710.2387230.9640.96797.7870.218
3.489-3.6970.478200.3496330.3536830.9030.93695.60760.33
3.697-3.9480.281630.2415760.2456460.960.96698.91640.235
3.948-4.2570.326170.1995530.2026080.9550.97693.750.184
4.257-4.6540.232280.154990.1555330.9740.98598.87430.157
4.654-5.1860.16940.1764810.1764930.9950.98298.37730.188
5.186-5.9560.21410.2094380.2094460.97498.43050.22
5.956-7.2180.324200.243510.2453750.9440.97198.93330.25
7.218-9.9010.195160.182750.1812930.9770.97999.31740.198
9.901-28.7840.16840.2171740.2151850.9920.97196.21620.238
Refinement TLS params.Method: refined / Origin x: 3.3122 Å / Origin y: 28.388 Å / Origin z: 1.1378 Å
111213212223313233
T0.2158 Å20.0194 Å20.0115 Å2-0.044 Å2-0.023 Å2--0.1728 Å2
L3.3297 °2-0.9694 °2-0.4289 °2-4.1406 °20.6858 °2--4.6371 °2
S0.1329 Å °0.347 Å °-0.4856 Å °-0.091 Å °-0.1122 Å °0.236 Å °0.8813 Å °-0.0901 Å °-0.0207 Å °
Refinement TLS groupSelection: ALL

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