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

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Basic information

Entry
Database: PDB / ID: 1gkp
TitleD-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space group C2221
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 / SYNCHROTRON / MAD / Resolution: 1.295 Å
AuthorsAbendroth, J. / Niefind, K. / Schomburg, D.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization, Preliminary X-Ray Analysis of a Native and Selenomethionine D-Hydantoinase from Thermus Sp
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 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_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
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
E: HYDANTOINASE
F: HYDANTOINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,81529
Polymers304,6896
Non-polymers2,12623
Water66,9443716
1
A: HYDANTOINASE
B: HYDANTOINASE
hetero molecules

A: HYDANTOINASE
B: HYDANTOINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,03316
Polymers203,1264
Non-polymers90812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
2
C: HYDANTOINASE
D: HYDANTOINASE
E: HYDANTOINASE
F: HYDANTOINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,79821
Polymers203,1264
Non-polymers1,67217
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.200, 215.900, 207.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9828, -0.0139, -0.1839), (-0.0104, -0.9997, 0.0201), (-0.1842, -0.0178, -0.9827)11.0417, 215.1449, 104.543
2given(0.4939, 0.8683, -0.0459), (0.8688, -0.4949, -0.0322), (-0.0362, -0.0322, -0.9988)-60.6443, 107.2622, 73.0192
3given(0.4972, -0.8673, -0.0242), (0.8556, 0.4948, -0.1521), (0.1439, 0.0549, 0.9881)125.6756, 7.4831, -39.1094
4given(0.4975, 0.866, -0.0501), (0.8563, -0.4995, -0.1311), (-0.1386, 0.0223, -0.9901)-58.9368, 115.5779, 170.4929
5given(0.4903, -0.8703, -0.046), (0.8708, 0.4914, -0.0162), (0.0367, -0.0321, 0.9988)128.6326, 2.4451, 73.5475

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Components

#1: Protein
HYDANTOINASE / DIHYDROPYRIMIDINASE


Mass: 50781.422 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: KCX IS A NZ-CARBOXYLATED LYSINE / Source: (gene. exp.) THERMUS SP. (bacteria) / 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.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3716 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 41 %
Description: MAD DATA TO 3AA, INITIAL MODEL FROM ARP AT 1.7AA
Crystal growpH: 7.5
Details: 1.65 MM AMMONIUM SULPHATE, 100 MM HEPES/NAOH PH 7.5, 5% (V/V) PEG 400, CRYO-BUFFER: 2 M LITHIUM SULPHATE, 100 MM HEPES/NAOH PH 7.5, 5% (V/V) PEG 400
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.65 Mammonium sulfate1reservoir
25 %PEG4001reservoir
3100 mMHEPES-NaOH1reservoirpH7.5
44.5 mg/mlprotein1drop
510 mg/mlSe-Met-protein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.842
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 24, 2000
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.842 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 693388 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 17.7
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.4 / % possible all: 98
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 2976914
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOFOR INDEXINGdata reduction
PROWFOR INTEGRATIONdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMphasing
ARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.295→50 Å / SU B: 1.996 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.18367 13809 2 %RANDOM
Rwork0.1529 ---
obs0.15352 679113 99.7 %-
Refinement stepCycle: LAST / Resolution: 1.295→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21456 0 87 3716 25259
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.184 / Rfactor Rwork: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_chiral_restr0.132

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