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- PDB-1gkq: D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space gr... -

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Basic information

Entry
Database: PDB / ID: 1gkq
TitleD-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space group P212121
ComponentsHYDANTOINASE
KeywordsHYDROLASE / HYDANTOINASE / DIHYDROPYRIMIDINASE / CYCLIC AMIDASE
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / metal ion binding / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / : / 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 ...Hydantoinase/dihydropyrimidinase / : / 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 speciesTHERMUS SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAbendroth, J. / Niefind, K. / Schomburg, D.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: X-Ray Structure of a Dihydropyrimidinase from Thermus Sp. At 1.3 A Resolution
Authors: Abendroth, J. / Niefind, K. / Schomburg, D.
History
DepositionAug 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
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: HYDANTOINASE
B: HYDANTOINASE
C: HYDANTOINASE
D: HYDANTOINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,64912
Polymers203,1264
Non-polymers5238
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.200, 161.500, 168.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.83138, -0.43383, -0.34726), (-0.43539, -0.89685, 0.07807), (-0.34531, 0.08628, -0.93451)45.05894, 298.81027, -136.96854
2given(-0.99419, 0.08167, -0.07018), (0.07805, 0.09756, -0.99216), (-0.07419, -0.99187, -0.10337)-87.79722, 93.40311, 96.19364
3given(-0.83595, 0.36147, 0.41296), (0.36054, -0.2056, 0.9098), (0.41377, 0.90943, 0.04155)-100.28361, 261.60437, -188.61897

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Components

#1: Protein
HYDANTOINASE / DIHYDROPYRIMIDINASE


Mass: 50781.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: KCX IS A NZ-CARBOXYLATED LYSINE / Source: (gene. exp.) THERMUS SP. (bacteria) / Description: RECOMBINANTLY EXPRESSED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q7SIE9*PLUS, 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.: 489 / 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: 2.8 Å3/Da / Density % sol: 61 %
Crystal growpH: 6.5
Details: 30% (W/V) PEG 6000, 100 MM CACODYLATE/HCL PH 6.5, 200 MM SODIUM ACETATE
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 %PEG60001reservoir
2100 mMcacodylate1reservoirpH6.5
3200 mMsodium acetate1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC SCIENCE DIP-2030H / Detector: IMAGE PLATE / Date: Nov 6, 1997
RadiationMonochromator: NI FITER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 70394 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 25 Å / % possible obs: 99.9 % / Num. measured all: 416020
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GKP

1gkp


Resolution: 2.6→25 Å / Rfactor Rfree error: 0.0035 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 3556 5 %RANDOM
Rwork0.1876 ---
obs0.1876 70394 99.8 %-
Solvent computationBsol: 42.4 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.335 Å20 Å20 Å2
2---6.564 Å20 Å2
3---4.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14304 0 8 489 14801
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.36
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.178
X-RAY DIFFRACTIONc_mcangle_it1.949
X-RAY DIFFRACTIONc_scbond_it2.158
X-RAY DIFFRACTIONc_scangle_it3.238
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 300 Å
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.289 332 4.77 %
Rwork0.249 6602 -
obs--99.7 %
Refinement
*PLUS
Rfactor Rfree: 0.211 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_plane_restr0.69
X-RAY DIFFRACTIONc_chiral_restr0.106

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