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- PDB-3dc8: Crystal structure of dihydropyrimidinase from Sinorhizobium meliloti -

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Basic information

Entry
Database: PDB / ID: 3dc8
TitleCrystal structure of dihydropyrimidinase from Sinorhizobium meliloti
ComponentsDihydropyrimidinase
KeywordsHYDROLASE / TIM-barrel
Function / homology
Function and homology information


pyrimidine-containing compound metabolic process / dihydropyrimidinase / dihydropyrimidinase activity / nucleobase-containing small molecule metabolic process / metal ion binding / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / : / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / D-hydantoinase/dihydropyrimidinase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S.
Citation
Journal: J.Struct.Biol. / Year: 2010
Title: Structure of dihydropyrimidinase from Sinorhizobium meliloti CECT4114: new features in an amidohydrolase family member
Authors: Martinez-Rodriguez, S. / Martinez-Gomez, A.I. / Clemente-Jimenez, J.M. / Rodriguez-Vico, F. / Garcia-Ruiz, J.M. / Las Heras-Vazquez, F.J. / Gavira, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary crystallographic studies of the recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114
Authors: Martinez-Rodriguez, S. / Gonzalez-Ramirez, L.A. / Clemente-Jimenez, J.M. / Rodriguez-Vico, F. / Las Heras-Vazquez, F.J. / Gavira, J.A. / Garcia-Ruiz, J.M.
History
DepositionJun 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 1, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_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
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydropyrimidinase
B: Dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,82912
Polymers107,0812
Non-polymers74810
Water24,1041338
1
A: Dihydropyrimidinase
B: Dihydropyrimidinase
hetero molecules

A: Dihydropyrimidinase
B: Dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,65824
Polymers214,1624
Non-polymers1,49620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area17440 Å2
ΔGint-374 kcal/mol
Surface area57140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.887, 126.281, 196.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1204-

HOH

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Components

#1: Protein Dihydropyrimidinase


Mass: 53540.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: CECT4114 / Gene: dhp / Plasmid: pBSK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q0PQZ5, dihydropyrimidinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1338 / 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: 3.61 Å3/Da / Density % sol: 65.93 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 4.6
Details: 4.0M sodium formate, 0.1M sodium acetate, pH 4.6, COUNTER-DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 31, 2006 / Details: Montel mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→39.89 Å / Num. obs: 129593 / % possible obs: 98.4 % / Redundancy: 3.47 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.0662 / Net I/σ(I): 13
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 1.83 % / Mean I/σ(I) obs: 3.11 / Num. unique all: 8930 / Rsym value: 0.311 / % possible all: 89.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å39.89 Å
Translation3 Å39.89 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YNY, 1KCX, 1K1D

1yny

1kcx

1k1d


Resolution: 1.85→29.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.398 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The structure was refined also with COOT 0.2 and MolProbity
RfactorNum. reflection% reflectionSelection details
Rfree0.176 6524 5 %RANDOM
Rwork0.148 ---
obs0.149 129519 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7313 0 36 1338 8687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0227588
X-RAY DIFFRACTIONr_bond_other_d0.0010.023
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.94610312
X-RAY DIFFRACTIONr_angle_other_deg0.33236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.55984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22623.799329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.217151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5851549
X-RAY DIFFRACTIONr_chiral_restr0.1460.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025776
X-RAY DIFFRACTIONr_nbd_refined0.2020.23856
X-RAY DIFFRACTIONr_nbd_other0.1350.23
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.21214
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.258
X-RAY DIFFRACTIONr_mcbond_it0.9181.54973
X-RAY DIFFRACTIONr_mcangle_it1.16827715
X-RAY DIFFRACTIONr_scbond_it2.02133046
X-RAY DIFFRACTIONr_scangle_it2.8354.52582
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 419 -
Rwork0.203 8073 -
all-8492 -
obs--88.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4189-0.2717-0.60421.8312-0.48991.3888-0.19870.37440.0706-0.41990.05210.2142-0.1066-0.08870.1467-0.0603-0.04770.0006-0.01560.0057-0.1311-33.335-9.358-40.951
25.88699.6521-2.42120.5239-4.50635.5912-0.16880.4235-0.4185-0.1115-0.0523-0.90620.33390.07070.2211-0.0823-0.0240.0161-0.0194-0.0527-0.1-28.913-17.173-43.252
31.19780.3549-0.24361.9279-1.18712.0931-0.03120.28690.0464-0.36140.03610.12920.2123-0.1449-0.0049-0.0799-0.0319-0.023-0.0499-0.0451-0.1018-37.843-14.848-34.366
40.6304-0.16150.23921.4574-2.86068.88520.03920.0333-0.0481-0.0188-0.01640.06910.38290.1762-0.0228-0.0871-0.05790.0121-0.0995-0.0337-0.0571-42.861-31.658-15.642
54.6692-1.83791.77841.3248-0.0131.46220.0339-0.2457-0.41090.12660.14980.22420.3372-0.3036-0.1837-0.0574-0.07780.011-0.0763-0.0127-0.0692-34.911-28.954-19.125
64.4155-1.66343.1970.877-0.4434.63030.06520.0327-0.48160.0590.03150.24070.452-0.1475-0.0967-0.0358-0.05790.0338-0.0967-0.0393-0.032-33.187-34.461-22.199
71.8541-1.09061.90356.5514-0.22012.7125-0.1077-0.0592-0.36650.70280.0224-0.13770.5950.1980.08520.0142-0.0075-0.0052-0.1344-0.0334-0.0185-19.01-36.074-12.346
80.9036-0.1242-0.55011.16110.69622.2284-0.0146-0.011-0.11680.1468-0.02320.02980.2622-0.10620.0378-0.0824-0.01510.0098-0.1472-0.0196-0.079-23.099-27.321-7.52
96.21.1181.43880.4687-0.25021.30610.0251-0.28930.00020.1656-0.04350.00130.04-0.18770.0184-0.0568-0.05360.0133-0.0784-0.0243-0.1037-41.515-22.8268.244
1010.35460.4294-3.66580.3578-0.11991.9462-0.0656-0.0260.16760.02110.04070.10490.0411-0.15560.0249-0.0875-0.0251-0.0144-0.1113-0.0076-0.1304-33.121-16.0112.578
113.2336-1.82-0.23551.66250.48061.64260.0021-0.02450.05990.0918-0.0053-0.0390.0321-0.00910.0032-0.1167-0.02930.0036-0.171-0.0018-0.1182-23.5-16.442-5.97
1217.0343.10441.57488.02350.20690.5749-0.3438-0.58990.90490.14650.10230.0596-0.4537-0.17310.2416-0.10890.021-0.0472-0.1203-0.0394-0.1207-24.281-7.389-4.846
131.82940.8612-0.55670.9896-0.21360.6879-0.0295-0.05150.06030.02410.01630.07720.0074-0.10540.0132-0.1174-0.0104-0.0044-0.1049-0.0142-0.113-39.1-12.74-8.425
143.23052.02141.8951.7612.663110.89020.0776-0.089-0.24540.199-0.02130.03260.5439-0.1688-0.0563-0.0931-0.05130.0283-0.129-0.0146-0.0609-50.538-29.064-2.803
150.37760.0984-0.07740.5048-0.20780.5737-0.01190.1032-0.0143-0.04540.00280.07540.0404-0.12990.0091-0.1276-0.0319-0.0061-0.092-0.0219-0.1194-35.09-12.611-24.921
1612.83958.5197-13.18956.5987-13.001332.6478-0.18150.79840.3516-0.25660.85420.49430.4654-1.1813-0.6727-0.10420.002-0.0237-0.01160.0179-0.0458-51.171-8.219-27.458
170.29990.0021-0.64970.8815-0.13911.465-0.01970.145-0.0063-0.02560.01340.14270.0092-0.23170.0063-0.1226-0.041-0.02970.0022-0.0101-0.0834-48.226-17.42-25.198
1810.3664-1.10163.52422.76970.07582.63810.08890.5117-0.0421-0.239-0.08060.18330.0933-0.1008-0.0084-0.0304-0.07560.0232-0.0359-0.0157-0.1462-39.332-26.077-32.47
199.06784.66736.23773.87772.4416.7429-0.15820.103-0.2525-0.00820.1416-0.20530.02160.21920.0166-0.11870.00230.0442-0.1214-0.0146-0.1146-8.995-17.671-16.062
204.8285-4.04564.61276.2827-4.69017.55660.03340.37260.2128-0.1935-0.1333-0.37230.26650.4130.0999-0.10030.071-0.01680.0188-0.0699-0.075910.466-22.2375.737
212.21520.3342-1.84380.3085-0.48145.1603-0.11190.1089-0.1443-0.1744-0.00820.00180.26570.00930.1201-0.0861-0.02050.0223-0.1134-0.0201-0.1282-11.153-10.848-39.27
223.42855.3002-0.646526.7206-3.39613.41250.07490.3614-0.228-0.7624-0.26210.00220.2361-0.06910.1872-0.0775-0.02120.009-0.0553-0.0343-0.1429-14.483-7.386-46.56
230.58670.0407-0.26791.97931.26811.8099-0.00070.0530.003-0.214-0.0395-0.0268-0.09680.06360.0402-0.1167-0.00790.0228-0.10650.0184-0.1403-6.375-0.815-36.19
242.65480.5026-0.89054.66880.57185.93430.055-0.31320.47760.4178-0.0414-0.0412-0.9578-0.2151-0.01360.1319-0.025-0.0158-0.017-0.0060.0252-2.18522.385-27.448
253.4147-1.4129-0.72992.93660.77480.7485-0.0191-0.06750.15580.03190.0492-0.0505-0.14980.066-0.0301-0.1016-0.02110.0158-0.10240.0057-0.1444-6.25310.508-32.004
2636.7344-1.950814.60267.6997-6.571222.4337-1.5245-0.5281.43441.1430.3328-1.0497-3.18090.2331.19170.4011-0.0582-0.1199-0.0820.00430.0278-16.34230.425-26.435
2717.0461-9.137-4.80418.33231.86464.37770.27010.14020.5868-0.5530.0109-0.6149-0.75280.3385-0.2810.0714-0.05810.0197-0.05190.05740.0122-12.56425.499-35.15
282.9178-1.2412-1.38812.61140.81491.39990.01460.1640.26940.03970.00910.0165-0.3405-0.0421-0.02370.010.0117-0.0159-0.10940.0441-0.0719-20.63222.847-30.047
290.554-0.02990.4771.0040.15192.8548-0.01090.02520.1028-0.0157-0.0095-0.0097-0.36550.12020.0204-0.0688-0.0049-0.0023-0.13270.0123-0.0937-22.22221.138-18.973
304.02111.1663-0.06381.39130.09320.01290.0309-0.15570.12030.0813-0.0205-0.0252-0.08980.0635-0.0103-0.0679-0.02950.015-0.099-0.023-0.1264-6.22621.54-3.307
312.8902-0.77240.25151.3912-0.45341.3953-0.0657-0.1425-0.01740.07130.04340.07-0.0124-0.00810.0223-0.1125-0.00360.0193-0.1579-0.013-0.1368-21.36510.14-11.026
321.64971.09290.14271.4588-0.00280.57880.02-0.1283-0.0080.0041-0.0062-0.0805-0.04390.0394-0.0138-0.0981-0.01530.023-0.134-0.0184-0.1405-5.1869.094-12.194
332.01990.79780.31710.65670.71111.2504-0.0596-0.06560.0223-0.00240.0296-0.0517-0.01920.13380.03-0.13160.00050.0119-0.1288-0.0067-0.1056-6.9536.473-13.914
349.93762.82571.21637.71377.936112.9559-0.54140.52290.1611-0.64120.47430.0164-0.41930.12650.0671-0.0491-0.112-0.0111-0.08540.0081-0.12736.34322.203-20.5
354.25111.1889-3.74873.09370.81957.89750.1450.12760.3638-0.25070.05870.1754-0.4525-0.2074-0.2037-0.0898-0.04920.01-0.1110.0172-0.05933.27425.815-12.607
360.5288-0.00450.04590.71270.01120.85120.02030.04170.0253-0.0335-0.0178-0.029-0.03380.0886-0.0025-0.1292-0.02030.019-0.1212-0.0112-0.1421-10.365-0.932-28.324
3731.344429.863513.528431.071816.516110.8611-0.32550.4074-0.1822-0.15110.5944-0.5527-0.04250.3844-0.2689-0.11150.00630.0307-0.068-0.0179-0.10365.33-6.975-29.077
380.38050.2240.33461.05330.42921.28870.03470.09410.0409-0.02130.0497-0.1205-0.0540.2535-0.0844-0.1002-0.02320.0313-0.0588-0.0254-0.09243.5863.989-30.295
394.10560.0075-1.8940.4026-0.25931.48090.07550.3520.0486-0.1096-0.0147-0.043-0.0776-0.1262-0.0608-0.0414-0.036-0.0107-0.1102-0.0225-0.1051-17.079.697-35.051
4030.6477-16.0537-27.268710.50116.088925.8201-0.03030.7913-0.2525-0.3662-0.53340.4079-0.2319-1.10780.5637-0.07450.0112-0.0162-0.0415-0.06880.0661-47.94412.266-12.073
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 242 - 24
2X-RAY DIFFRACTION2AA25 - 3125 - 31
3X-RAY DIFFRACTION3AA32 - 6032 - 60
4X-RAY DIFFRACTION4AA61 - 7661 - 76
5X-RAY DIFFRACTION5AA77 - 9977 - 99
6X-RAY DIFFRACTION6AA100 - 121100 - 121
7X-RAY DIFFRACTION7AA122 - 140122 - 140
8X-RAY DIFFRACTION8AA141 - 182141 - 182
9X-RAY DIFFRACTION9AA183 - 206183 - 206
10X-RAY DIFFRACTION10AA207 - 219207 - 219
11X-RAY DIFFRACTION11AA220 - 242220 - 242
12X-RAY DIFFRACTION12AA243 - 249243 - 249
13X-RAY DIFFRACTION13AA250 - 316250 - 316
14X-RAY DIFFRACTION14AA317 - 331317 - 331
15X-RAY DIFFRACTION15AA332 - 394332 - 394
16X-RAY DIFFRACTION16AA395 - 401395 - 401
17X-RAY DIFFRACTION17AA402 - 434402 - 434
18X-RAY DIFFRACTION18AA435 - 452435 - 452
19X-RAY DIFFRACTION19AA453 - 470453 - 470
20X-RAY DIFFRACTION20AA471 - 484471 - 484
21X-RAY DIFFRACTION21BB2 - 232 - 23
22X-RAY DIFFRACTION22BB24 - 3424 - 34
23X-RAY DIFFRACTION23BB35 - 6035 - 60
24X-RAY DIFFRACTION24BB61 - 7461 - 74
25X-RAY DIFFRACTION25BB75 - 9175 - 91
26X-RAY DIFFRACTION26BB92 - 9992 - 99
27X-RAY DIFFRACTION27BB100 - 111100 - 111
28X-RAY DIFFRACTION28BB112 - 140112 - 140
29X-RAY DIFFRACTION29BB141 - 182141 - 182
30X-RAY DIFFRACTION30BB183 - 217183 - 217
31X-RAY DIFFRACTION31BB218 - 249218 - 249
32X-RAY DIFFRACTION32BB250 - 281250 - 281
33X-RAY DIFFRACTION33BB282 - 316282 - 316
34X-RAY DIFFRACTION34BB317 - 322317 - 322
35X-RAY DIFFRACTION35BB323 - 334323 - 334
36X-RAY DIFFRACTION36BB335 - 394335 - 394
37X-RAY DIFFRACTION37BB395 - 399395 - 399
38X-RAY DIFFRACTION38BB400 - 436400 - 436
39X-RAY DIFFRACTION39BB437 - 464437 - 464
40X-RAY DIFFRACTION40BB465 - 477465 - 477

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