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- PDB-1nfg: Structure of D-hydantoinase -

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Basic information

Entry
Database: PDB / ID: 1nfg
TitleStructure of D-hydantoinase
ComponentsD-hydantoinase
KeywordsHYDROLASE / TIM barrel
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amides / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / metal ion binding / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / : / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases ...Hydantoinase/dihydropyrimidinase / : / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / 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 speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsXu, Z. / Yang, Y. / Jiang, W. / Arnold, E. / Ding, J.
CitationJournal: J.Bacteriol. / Year: 2003
Title: Crystal Structure of D-Hydantoinase from Burkholderia pickettii at a Resolution of 2.7 Angstroms: Insights into the Molecular Basis of Enzyme Thermostability.
Authors: Xu, Z. / Liu, Y. / Yang, Y. / Jiang, W. / Arnold, E. / Ding, J.
History
DepositionDec 14, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn_type / struct_ref_seq_dif / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-hydantoinase
B: D-hydantoinase
C: D-hydantoinase
D: D-hydantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,68312
Polymers200,1594
Non-polymers5238
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9890 Å2
ΔGint-335 kcal/mol
Surface area57470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.7, 170.5, 87.3
Angle α, β, γ (deg.)90.0, 95.2, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-hydantoinase / Dihydropyrimidinase / DHPase


Mass: 50039.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Plasmid: pXZPH2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8VTT5, 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.: 504 / 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: 2.5 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG6000, 0.1M Bicine, 0.005M CdCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
250 mMimidazole1drop
3100 mM1dropNaCl
415 mg/mlprotein1drop
516 %PEG60001reservoir
60.1 MBicine1reservoir
70.005 M1reservoirpH8.5CdCl2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 11, 2002 / Details: confocal mirror
RadiationMonochromator: Confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. all: 139372 / Num. obs: 53883 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 47.2 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 3 / Num. unique all: 5481 / % possible all: 96.8
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 139372
Reflection shell
*PLUS
Lowest resolution: 2.78 Å / % possible obs: 96.8 %

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CrystalClear(MSC/RIGAKU)data reduction
CNSrefinement
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GKQ

1gkq


Resolution: 2.7→14.94 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2681 -RANDOM
Rwork0.22 ---
all0.221 53756 --
obs0.221 53756 98.3 %-
Solvent computationSolvent model: flat model / Bsol: 32.0895 Å2 / ksol: 1.4629 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.7→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14052 0 8 504 14564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.7-2.870.31484500.2978X-RAY DIFFRACTION89926
2.87-3.090.31114270.2808X-RAY DIFFRACTION90186
3.09-3.390.26954710.2577X-RAY DIFFRACTION90376
3.39-3.880.2444360.2231X-RAY DIFFRACTION89356
3.88-4.860.18554740.1723X-RAY DIFFRACTION89556
4.86-14.940.2034230.1741X-RAY DIFFRACTION88196
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 15 Å / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.78 Å / Rfactor Rfree: 0.324 / Num. reflection Rfree: 221 / Rfactor Rwork: 0.303 / Num. reflection obs: 4281

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