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- PDB-5vgm: Crystal structure of dihydroorotase pyrC from Vibrio cholerae in ... -

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Basic information

Entry
Database: PDB / ID: 5vgm
TitleCrystal structure of dihydroorotase pyrC from Vibrio cholerae in complex with zinc at 1.95 A resolution.
ComponentsDihydroorotase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


dihydroorotase / pyrimidine ribonucleotide biosynthetic process / pyrimidine nucleobase biosynthetic process / pyrimidine nucleotide biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / cytosol / cytoplasm
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
ACETATE ION / Dihydroorotase / Dihydroorotase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLipowska, J. / Shabalin, I.G. / Miks, C.D. / Winsor, J. / Cooper, D.R. / Shuvalova, L. / Kwon, K. / Lewinski, K. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.
Authors: Lipowska, J. / Miks, C.D. / Kwon, K. / Shuvalova, L. / Zheng, H. / Lewinski, K. / Cooper, D.R. / Shabalin, I.G. / Minor, W.
History
DepositionApr 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 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: Dihydroorotase
B: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,24111
Polymers75,7082
Non-polymers5339
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-177 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.507, 57.257, 87.524
Angle α, β, γ (deg.)90.000, 105.090, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 0 - 342 / Label seq-ID: 3 - 345

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dihydroorotase / / DHOase


Mass: 37853.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: pyrC, BSN91_03690, EN12_18175, ERS013140_03537, ERS013198_00138, ERS013199_01662
Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 "magic"
References: UniProt: A0A0H6AFA4, UniProt: Q9KL24*PLUS, dihydroorotase
#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 / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCE, and 20 mM L-citruline were mixed with 0.2 ul of the Top96 screen condition #C11 (0. ...Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCE, and 20 mM L-citruline were mixed with 0.2 ul of the Top96 screen condition #C11 (0.2 M Sodium Acetate 0.1 M Sodium Cacodylate: HCl, pH 6.5 30 % (w/v) PEG 8000), 0.1 ul of the Hampton Additive screen # 94 (7%v/v 1-Butanol) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 1 hours.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 41257 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 32.8 Å2 / CC1/2: 0.87 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Rsym value: 0.063 / Χ2: 1.361 / Net I/av σ(I): 19.7 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
1.95-1.982.60.3722.313530.8710.2570.4540.3721.02362.5
1.98-2.022.70.3490.8970.2350.4221.02875.9
2.02-2.062.90.3550.8760.2360.4281.10882.6
2.06-2.13.10.3280.9190.2120.3921.0691
2.1-2.153.20.30.9250.1920.3571.16194.7
2.15-2.23.30.2850.9360.1820.3391.17897.5
2.2-2.253.30.2860.9260.1810.3391.48198.8
2.25-2.313.40.2520.4070.1650.3031.49299
2.31-2.383.50.2010.9660.1250.2371.34499.7
2.38-2.463.50.1750.9770.1090.2061.35799.5
2.46-2.543.50.150.9830.0930.1771.47899.7
2.54-2.653.60.1370.9810.0850.1611.40399.4
2.65-2.773.50.1130.9850.0710.1341.40799.5
2.77-2.913.50.0970.9870.0610.1151.48499.5
2.91-3.093.50.0790.9910.050.0941.52999.5
3.09-3.333.40.0680.9920.0440.0811.5398.8
3.33-3.663.40.0550.9940.0360.0661.52897.9
3.66-4.193.30.0470.9950.0310.0571.36596.3
4.19-5.263.30.0420.9960.0270.051.31994.6
5.26-203.30.0450.9970.0280.0531.38795.2

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Processing

Software
NameVersionClassification
MD2data collection
SCALEPACKdata scaling
HKL-3000data reduction
MOLREPphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V0G

5v0g
PDB Unreleased entry


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 10.361 / SU ML: 0.137 / SU R Cruickshank DPI: 0.1877 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.152
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2077 5 %RANDOM
Rwork0.1676 ---
obs0.1695 39091 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.81 Å2 / Biso mean: 48.505 Å2 / Biso min: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å20.65 Å2
2--5.04 Å2-0 Å2
3----4.96 Å2
Refinement stepCycle: final / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5118 0 21 227 5366
Biso mean--68.15 53.42 -
Num. residues----673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195272
X-RAY DIFFRACTIONr_bond_other_d0.0070.024859
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9577175
X-RAY DIFFRACTIONr_angle_other_deg0.971311195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15723.628215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70815795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2361530
X-RAY DIFFRACTIONr_chiral_restr0.0750.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215870
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021052
X-RAY DIFFRACTIONr_sphericity_bonded20.35854
Refine LS restraints NCS

Ens-ID: 1 / Number: 21036 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 130 -
Rwork0.267 2003 -
all-2133 -
obs--67.18 %
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)
12.4383-0.38180.37983.22281.61872.39390.0167-0.0624-0.10950.1914-0.10640.1460.3321-0.48370.08970.3514-0.12540.01680.23910.00440.283714.72615.94486.798
25.41191.5681.36783.84930.79694.56330.0286-0.09630.20490.0389-0.1329-0.0235-0.1081-0.10280.10430.26470.0128-0.00910.2378-0.02960.238116.62227.65795.924
31.82150.7254-1.37194.77270.9683.61520.01440.20710.1802-0.1744-0.1599-0.1715-0.1991-0.08280.14550.24370.0053-0.05040.2056-0.00240.291827.91530.29896.235
40.77050.2378-0.53770.0766-0.13798.4452-0.0952-0.1204-0.028-0.0389-0.0297-0.0343-0.59740.32160.12480.37340.0057-0.0540.16210.0120.304934.99930.29288.049
51.6302-0.07750.41170.9006-0.4012.3811-0.0309-0.1156-0.11980.1343-0.0174-0.02240.1935-0.00770.04830.279-0.0177-0.0390.0523-0.02160.265927.84918.53477.148
61.88010.32330.94361.66760.56742.11590.1504-0.0097-0.33790.2781-0.070.07510.4708-0.0819-0.08040.4155-0.10730.00490.1394-0.00020.355519.947.53980.836
71.5890.79620.38652.27930.66071.329-0.01920.03280.0216-0.1002-0.02860.1686-0.0796-0.2480.04780.11720.0052-0.09670.16250.00510.243825.59742.26140.807
84.6647-2.5602-0.42296.66460.54823.4142-0.01070.084-0.389-0.06680.0345-0.02490.38920.0653-0.02380.1484-0.0486-0.07170.1922-0.050.26536.88427.28335.72
93.2505-1.3717-0.27433.80370.75053.509-0.0080.042-0.2738-0.02010.0411-0.09890.05410.2274-0.03320.1361-0.0344-0.07940.12-0.05580.274143.15727.51640.415
101.5384-0.2144-0.92610.73580.78722.8544-0.0917-0.0717-0.12690.0970.0504-0.19640.26430.31630.04140.13340.0273-0.07610.0748-0.01680.29144.87431.45751.615
111.22790.2954-0.51531.5199-0.36131.26420.02550.03510.01570.1504-0.05890.05090.0738-0.07410.03330.1341-0.0151-0.07470.0509-0.02420.223330.25237.34658.65
121.67690.2637-0.31381.11890.21570.69530.0016-0.02050.16180.0028-0.00480.0853-0.0991-0.18110.00330.13040.0246-0.1080.07440.00870.267129.4950.34451.329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 51
2X-RAY DIFFRACTION2A52 - 118
3X-RAY DIFFRACTION3A119 - 140
4X-RAY DIFFRACTION4A141 - 171
5X-RAY DIFFRACTION5A172 - 280
6X-RAY DIFFRACTION6A281 - 342
7X-RAY DIFFRACTION7B-2 - 68
8X-RAY DIFFRACTION8B69 - 118
9X-RAY DIFFRACTION9B119 - 140
10X-RAY DIFFRACTION10B141 - 197
11X-RAY DIFFRACTION11B198 - 270
12X-RAY DIFFRACTION12B271 - 342

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