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- PDB-1gkr: L-Hydantoinase (Dihydropyrimidinase) from Arthrobacter aurescens -

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Basic information

Entry
Database: PDB / ID: 1gkr
TitleL-Hydantoinase (Dihydropyrimidinase) from Arthrobacter aurescens
ComponentsNON-ATP DEPENDENT L-SELECTIVE HYDANTOINASE
KeywordsHYDROLASE / HYDANTOINASE / DIHYDROPYRIMIDINASE / CYCLIC AMIDASE
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amides / allantoin catabolic process / allantoinase activity / purine nucleobase catabolic process / cobalt ion binding / zinc ion binding / cytoplasm
Similarity search - Function
Allantoinase / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll ...Allantoinase / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesARTHROBACTER AURESCENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAbendroth, J. / Niefind, K. / Schomburg, D.
Citation
Journal: Biochemistry / Year: 2002
Title: The structure of L-hydantoinase from Arthobacter aurescens leads to an understanding of dihydropyrimidinase substrate and enantio specificity.
Authors: Abendroth, J. / Niefind, K. / May, O. / Siemann, M. / Syldatk, C. / Schomburg, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary X-Ray Analysis of a Hydantoinase from Arthrobacter Aurescens Dsm 3745.
Authors: May, O. / Siemann, M. / Syldatk, C. / Niefind, K. / Schomburg, D.
History
DepositionAug 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / pdbx_database_status / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NON-ATP DEPENDENT L-SELECTIVE HYDANTOINASE
B: NON-ATP DEPENDENT L-SELECTIVE HYDANTOINASE
C: NON-ATP DEPENDENT L-SELECTIVE HYDANTOINASE
D: NON-ATP DEPENDENT L-SELECTIVE HYDANTOINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,29712
Polymers198,7744
Non-polymers5238
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-342.74 kcal/mol
Surface area60200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.500, 74.300, 146.900
Angle α, β, γ (deg.)90.00, 106.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.61834, 0.03539, -0.78512), (0.04414, -0.99898, -0.01027), (-0.78467, -0.02831, -0.61926)-10.228, -158.01401, -28.975
2given(-0.63294, -0.20306, 0.7471), (-0.20356, -0.88739, -0.41365), (0.74696, -0.4139, 0.52033)75.041, -153.66499, -78.695
3given(-0.9835, 0.17717, 0.03648), (0.17592, 0.88995, 0.42077), (0.04208, 0.42024, -0.90644)92.994, -0.912, -37.003

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Components

#1: Protein
NON-ATP DEPENDENT L-SELECTIVE HYDANTOINASE / HYDANTOINASE


Mass: 49693.445 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: DSM 3745 / Source: (natural) ARTHROBACTER AURESCENS (bacteria) / References: UniProt: P81006, dihydropyrimidinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.2 Å3/Da / Density % sol: 63 %
Crystal growpH: 8.5
Details: 16-18% (W/V) PEG 8000, 250 MM LITHIUM SULPHATE, 100 MM MES/TRIS PH 8.5
Crystal grow
*PLUS
Temperature: 292 K / pH: 8 / Method: vapor diffusion, sitting drop
Details: May, O., (1996) Acta Crystallogr.,Sect.D, D52, 1209.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
116-18 %(w/v)PEG80001reservoir
20.25 M1reservoirLi2SO4
30.5 mM1reservoirMnCl2
40.1 MMES1reservoirpH8.5
510 mg/mlL-hydantoinase1drop
60.1 MTris1droppH8.0

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 20, 1996
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 61763 / % possible obs: 86.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 2.5 / % possible all: 41.2
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. measured all: 124261
Reflection shell
*PLUS
% possible obs: 41.2 %

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Processing

Software
NameVersionClassification
CNS1refinement
XENGENdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL FROM PDB ENTRY 1GKP

1gkp


Resolution: 2.6→30 Å / Rfactor Rfree error: 0.0043 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE STRUCTURE HAS BEEN REFINED WITH ONLY ONE CHAIN USING THE NCS MATRICES GIVEN BELOW
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3106 4.4 %RANDOM
Rwork0.224 ---
obs0.224 61515 86.3 %-
Solvent computationBsol: 30.7 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1-11.032 Å20 Å2-0.884 Å2
2---12.42 Å20 Å2
3---1.388 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13680 0 8 508 14196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.333 94 1.3 %
Rwork0.334 1823 -
obs--27.1 %
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12

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