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- PDB-3gri: The Crystal Structure of a Dihydroorotase from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 3gri
TitleThe Crystal Structure of a Dihydroorotase from Staphylococcus aureus
ComponentsDihydroorotase
KeywordsHYDROLASE / IDP00795 / Metal-binding / Pyrimidine biosynthesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


dihydroorotase / dihydroorotase activity / 'de novo' UMP biosynthetic process / zinc ion binding
Similarity search - Function
Dihydroorotase / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases ...Dihydroorotase / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / 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 speciesStaphylococcus aureus subsp. aureus MW2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The Crystal Structure of a Dihydroorotase from Staphylococcus aureus
Authors: Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F.
History
DepositionMar 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroorotase
B: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,09711
Polymers93,6992
Non-polymers3979
Water8,611478
1
A: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0666
Polymers46,8501
Non-polymers2165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0315
Polymers46,8501
Non-polymers1814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.217, 55.229, 85.647
Angle α, β, γ (deg.)88.33, 76.56, 76.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Dihydroorotase / / DHOase


Mass: 46849.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus MW2 (bacteria)
Strain: aureus COL / Gene: MW1084, pyrC, pyrC SACOL1213 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 De3 / References: UniProt: P65907, dihydroorotase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 2M Ammonium Sulphate, 5% Iso-propanol, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97923 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2009 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 54638 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.083
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.652 / % possible all: 94.1

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIXSHARPmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.514 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS Refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.23673 2934 5.1 %RANDOM
Rwork0.18869 ---
obs0.19117 54638 97.77 %-
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: 26.698 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.36 Å2-0.34 Å2
2--1.42 Å20.51 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6459 0 9 478 6946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226590
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9688943
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4925845
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73325.31290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.131151104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6891526
X-RAY DIFFRACTIONr_chiral_restr0.0950.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025002
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.23236
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24532
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2519
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1920.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1230.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7421.54325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98626779
X-RAY DIFFRACTIONr_scbond_it2.03632511
X-RAY DIFFRACTIONr_scangle_it2.8714.52164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 207 -
Rwork0.227 3994 -
obs--96.51 %
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)
18.1612.7512-1.70152.3103-2.07081.97570.4245-1.2343-1.4385-0.3037-1.03-0.91280.61420.3190.60550.00590.09130.17110.04640.45220.813882.31811.21340.4538
21.95020.4651-0.38241.6815-0.17930.35690.0498-0.8749-0.3532-0.0347-0.1274-0.19580.00070.16090.0776-0.1050.02670.02090.09720.14-0.042569.569923.852643.9306
32.6735-0.43940.50281.9776-1.74243.6718-0.0923-0.66440.0038-0.0382-0.0999-0.0349-0.25240.15270.1922-0.1145-0.00360.00350.0653-0.0468-0.107777.029836.769839.0825
41.765-5.59323.050523.4916-20.564325.8635-0.2838-0.77660.13740.84850.8720.7895-0.9797-1.2389-0.5882-0.06250.04060.0170.0704-0.1262-0.014265.045342.723629.3661
59.38180.53980.1750.6922-0.07942.3722-0.0469-0.0886-0.0111-0.0424-0.1093-0.0466-0.1450.02860.1563-0.0010.010.0129-0.1549-0.0851-0.107270.47138.305225.7014
61.8387-0.2573-0.12960.4419-0.50821.3592-0.0065-0.2251-0.299-0.16290.0310.02460.0844-0.0669-0.02460.0014-0.00770.0164-0.1538-0.0323-0.044654.927527.818727.9093
71.70540.0563-0.33561.3004-0.50551.8046-0.0326-0.4986-0.5032-0.1791-0.0609-0.06510.25730.01920.0936-0.09010.01440.0238-0.1210.1002-0.019361.922218.551837.1583
84.70210.47-1.052.8992-0.37422.44240.0143-0.7523-0.87910.0428-0.287-0.40190.24740.20420.2727-0.14620.03250.0135-0.02940.31510.075967.657811.58244.8812
94.1866-0.59853.65953.3971-0.4115.37240.16491.10510.0446-0.4843-0.22510.40860.11850.09680.0602-0.0946-0.0337-0.03950.203-0.0003-0.215332.985846.6434-24.6815
102.76330.76821.34740.90380.8071.5904-0.17330.55130.5964-0.01070.00160.1002-0.03890.17020.1717-0.0536-0.0467-0.0287-0.04640.0925-0.019145.987258.0098-5.8623
112.5209-0.34141.85981.7928-1.61525.583-0.14390.18020.64770.23390.0763-0.0662-0.1267-0.02610.0675-0.0173-0.0072-0.0323-0.197-0.05740.086539.566860.75347.3297
122.9426-2.2273.64093.4604-3.55636.4081-0.34740.00990.34090.36420.0902-0.1071-0.43240.10020.25730.0458-0.0202-0.0183-0.1816-0.1383-0.05342.129752.472615.3297
137.76040.9362-0.43721.2704-0.07280.9217-0.2115-0.0526-0.00980.0261-0.0517-0.10740.0444-0.13290.26320.04270.01080.0061-0.1656-0.1029-0.075244.694545.757815.5547
142.32760.58710.18460.487-0.19280.7851-0.04410.33720.08420.04290.0353-0.04670.07030.040.00890.01990.01060.03-0.1142-0.0605-0.079561.143644.65955.0184
152.15530.27230.60350.98440.20390.8625-0.08420.69510.3136-0.0133-0.0141-0.04560.0770.07370.0983-0.0784-0.02830.0060.08040.0274-0.156550.627649.7102-8.2956
162.93730.1873-0.48771.26570.23750.7134-0.14351.18090.6848-0.24280.0029-0.0185-0.20610.10530.1406-0.0535-0.0677-0.0270.26190.2465-0.048251.727858.2295-16.7333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 47
2X-RAY DIFFRACTION2A48 - 94
3X-RAY DIFFRACTION3A95 - 147
4X-RAY DIFFRACTION4A148 - 160
5X-RAY DIFFRACTION5A161 - 181
6X-RAY DIFFRACTION6A182 - 303
7X-RAY DIFFRACTION7A304 - 364
8X-RAY DIFFRACTION8A365 - 422
9X-RAY DIFFRACTION9B1 - 45
10X-RAY DIFFRACTION10B46 - 93
11X-RAY DIFFRACTION11B94 - 130
12X-RAY DIFFRACTION12B131 - 158
13X-RAY DIFFRACTION13B159 - 180
14X-RAY DIFFRACTION14B181 - 297
15X-RAY DIFFRACTION15B298 - 379
16X-RAY DIFFRACTION16B380 - 423

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