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- PDB-3jze: 1.8 Angstrom resolution crystal structure of dihydroorotase (pyrC... -

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Basic information

Entry
Database: PDB / ID: 3jze
Title1.8 Angstrom resolution crystal structure of dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
ComponentsDihydroorotase
KeywordsHYDROLASE / Dihydroorotase / pyrC / idp00873 / Metal-binding / Pyrimidine biosynthesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


dihydroorotase / pyrimidine nucleotide biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Dihydroorotase homodimeric type / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Amidohydrolase family / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / BETA-MERCAPTOETHANOL / TRIETHYLENE GLYCOL / Dihydroorotase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 23, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionSep 29, 2009ID: 3IHN
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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.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_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 22, 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: Dihydroorotase
B: Dihydroorotase
C: Dihydroorotase
D: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,02032
Polymers165,7524
Non-polymers2,26828
Water23,9241328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8.1 kcal/mol
Surface area25460 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-7.5 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.437, 79.486, 180.610
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydroorotase / DHOase


Mass: 41437.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: subsp. enterica serovar Typhimurium str. LT2 / Gene: pyrC, STM1163 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): DL21(DE3) / References: UniProt: P06204, dihydroorotase

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Non-polymers , 7 types, 1356 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1328 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein solution: 6.8 mg/mL, 0.25 Sodium chloride, Tris-HCl pH 8.3. Screen solution: PEGs II, condition B10, 0.1M Sodium acetate, 0.1M MES pH 6.5, 30% w/v PEG 2000 MME., VAPOR DIFFUSION, ...Details: Protein solution: 6.8 mg/mL, 0.25 Sodium chloride, Tris-HCl pH 8.3. Screen solution: PEGs II, condition B10, 0.1M Sodium acetate, 0.1M MES pH 6.5, 30% w/v PEG 2000 MME., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 130226 / Num. obs: 130226 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6322 / % possible all: 97.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EG6

2eg6


Resolution: 1.8→29.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.162 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic individual / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20301 6556 5 %RANDOM
Rwork0.16347 ---
all0.16547 123600 --
obs0.16547 123600 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.325 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0 Å2-0.58 Å2
2--1.74 Å2-0 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10728 0 112 1328 12168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02111446
X-RAY DIFFRACTIONr_bond_other_d0.0010.027657
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.95715532
X-RAY DIFFRACTIONr_angle_other_deg0.888318603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.87151438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.10623.284536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.604151821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5151595
X-RAY DIFFRACTIONr_chiral_restr0.0960.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022382
X-RAY DIFFRACTIONr_mcbond_it1.0221.57083
X-RAY DIFFRACTIONr_mcbond_other0.3461.52820
X-RAY DIFFRACTIONr_mcangle_it1.673211477
X-RAY DIFFRACTIONr_scbond_it2.82834363
X-RAY DIFFRACTIONr_scangle_it4.3344.54055
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 490 -
Rwork0.224 8794 -
obs-8794 95.82 %
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)
11.5912-0.4299-0.67111.7793-0.2542.08610.00920.0111-0.0142-0.17550.09980.13840.0072-0.3689-0.10910.0934-0.0647-0.03920.1560.00580.0738-1.863817.06245.306
21.2723-0.44650.13722.2507-0.4762.1254-0.0039-0.0805-0.07580.07940.08690.09480.2579-0.2329-0.0830.138-0.1033-0.02360.17250.00280.0926-0.27825.202416.705
30.51540.24810.2871.13760.2661.24870.02660.0469-0.0864-0.05980.0632-0.13430.1866-0.061-0.08980.0718-0.042-0.00390.0567-0.04610.084815.452213.889411.0958
40.4560.9282-0.24982.75961.20583.7399-0.02710.0512-0.0889-0.43890.0954-0.1862-0.5312-0.0947-0.06830.26220.027-0.0330.22510.00720.20237.916628.718-1.4542
51.8869-0.243-0.55951.2321-0.10251.7123-0.0006-0.03510.1301-0.00530.0219-0.0016-0.2104-0.0191-0.02130.09230.0075-0.03510.0115-0.02060.052233.29850.387733.3421
64.11091.91380.67341.5570.77950.949-0.1080.296-0.1217-0.15530.1369-0.065-0.01050.1671-0.02890.0564-0.00520.00020.0796-0.05120.105340.225831.690623.1661
71.09820.04040.28470.72860.12571.07920.0024-0.0777-0.13860.0960.0194-0.00040.0221-0.0572-0.02180.02680.0076-0.00560.01040.00350.040128.578833.027636.5405
82.91540.57890.98090.6824-0.06792.2274-0.0581-0.4129-0.27380.12160.07790.0527-0.1109-0.4119-0.01980.14880.05730.04780.2022-0.00750.202915.157839.569444.7572
90.86910.17650.07431.6482-0.19261.5307-0.00410.08110.03840.05410.06440.0962-0.1796-0.3314-0.06030.09970.08820.01870.13880.0060.069-26.328729.713279.6306
101.1185-0.8293-0.29131.49960.36511.33230.059-0.01160.1634-0.04840.0513-0.217-0.28220.003-0.11030.08490.0163-0.00060.034-0.02810.0992-7.043529.983774.6486
110.4401-0.2329-0.3820.94610.4611.42090.0066-0.05850.02570.18350.064-0.1187-0.0534-0.053-0.07060.08350.0323-0.03060.0386-0.0230.0656-11.933121.13384.7489
122.7063-0.25290.7771.98360.93543.81260.16630.0190.17790.4685-0.0449-0.09550.61-0.0699-0.12140.2479-0.005-0.00030.11820.03530.1493-16.8667.941588.7988
131.87410.13340.56471.054-0.00251.73760.00850.0424-0.17460.01490.0073-0.02120.1977-0.0186-0.01590.0913-0.01370.00670.0158-0.02780.05777.9652-10.391857.0846
142.2414-0.7421-0.33881.59340.57831.4293-0.0094-0.080.19560.02660.0231-0.1245-0.0470.1311-0.01380.032-0.0149-0.01310.0303-0.02660.081115.29568.120861.7183
151.1701-0.0505-0.41960.68780.33261.1565-0.00650.10770.1206-0.09810.00440.0346-0.0505-0.06250.00210.0246-0.0028-0.01870.01560.0040.0442-0.0436.99853.5241
163.1346-0.2959-1.53860.8510.30552.22690.03430.42370.3029-0.16650.04560.0999-0.0086-0.3662-0.07990.141-0.0331-0.070.17840.00050.1811-10.19430.569145.5183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 69
2X-RAY DIFFRACTION2A70 - 128
3X-RAY DIFFRACTION3A129 - 307
4X-RAY DIFFRACTION4A308 - 348
5X-RAY DIFFRACTION5B6 - 140
6X-RAY DIFFRACTION6B141 - 169
7X-RAY DIFFRACTION7B170 - 307
8X-RAY DIFFRACTION8B308 - 347
9X-RAY DIFFRACTION9C6 - 139
10X-RAY DIFFRACTION10C140 - 215
11X-RAY DIFFRACTION11C216 - 316
12X-RAY DIFFRACTION12C317 - 347
13X-RAY DIFFRACTION13D6 - 139
14X-RAY DIFFRACTION14D140 - 196
15X-RAY DIFFRACTION15D197 - 307
16X-RAY DIFFRACTION16D308 - 347

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