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- PDB-3mpg: Dihydroorotase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 3mpg
TitleDihydroorotase from Bacillus anthracis
ComponentsDihydroorotase
KeywordsHYDROLASE
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 speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSantarsiero, B.D. / Mehboob, S. / Johnson, M.E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of dihydroorotase from Bacillus anthracis at 2.6A resolution.
Authors: Mehboob, S. / Mulhearn, D.C. / Truong, K. / Johnson, M.E. / Santarsiero, B.D.
History
DepositionApr 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)93,6986
Polymers93,4372
Non-polymers2624
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-173 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.360, 80.784, 104.772
Angle α, β, γ (deg.)90.00, 100.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydroorotase / DHOase


Mass: 46718.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS3739, BA_4027, GBAA_4027, pyrC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81WF0, dihydroorotase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200mM MgCl2, 20%PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 25527 / Num. obs: 26859 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.55-2.592.50.263189.9
2.59-2.6430.283195.8
2.64-2.693.30.26197.1
2.69-2.753.90.26198.9
2.75-2.814.30.237199.6
2.81-2.874.50.232199.8
2.87-2.944.70.209199.6
2.94-3.024.70.172199.9
3.02-3.114.70.161100
3.11-3.214.70.136199.9
3.21-3.324.70.125199.9
3.32-3.464.70.1081100
3.46-3.614.60.096199.9
3.61-3.83.70.11193.6
3.8-4.044.40.079198.6
4.04-4.354.60.071199.8
4.35-4.784.60.069199.8
4.78-5.464.50.071199.9
5.46-6.834.50.071199.8
6.83-204.30.05199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.6 Å19.55 Å
Translation3.6 Å19.55 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1224 4.8 %random
Rwork0.212 ---
obs0.212 25265 99 %-
Solvent computationBsol: 47.446 Å2
Displacement parametersBiso mean: 47.531 Å2
Baniso -1Baniso -2Baniso -3
1-1.982 Å20 Å212.113 Å2
2--0.685 Å20 Å2
3----2.667 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 0 4 180 6694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.512
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID
2.6-2.640.3546560.2805X-RAY DIFFRACTION
2.64-2.680.3548500.2634X-RAY DIFFRACTION
2.68-2.720.3961450.3135X-RAY DIFFRACTION
2.72-2.760.3965470.2698X-RAY DIFFRACTION
2.76-2.810.3151530.2598X-RAY DIFFRACTION
2.81-2.860.3321360.2622X-RAY DIFFRACTION
2.86-2.920.3618530.2727X-RAY DIFFRACTION
2.92-2.980.3443580.2534X-RAY DIFFRACTION
2.98-3.040.4399510.2576X-RAY DIFFRACTION
3.04-3.110.4164510.2583X-RAY DIFFRACTION
3.11-3.190.2958510.2561X-RAY DIFFRACTION
3.19-3.270.3372510.2249X-RAY DIFFRACTION
3.27-3.370.3344510.2657X-RAY DIFFRACTION
3.37-3.480.2747380.2398X-RAY DIFFRACTION
3.48-3.60.3284600.2312X-RAY DIFFRACTION
3.6-3.740.3592370.2249X-RAY DIFFRACTION
3.74-3.910.2513560.1897X-RAY DIFFRACTION
3.91-4.120.2655640.1858X-RAY DIFFRACTION
4.12-4.370.247430.1764X-RAY DIFFRACTION
4.37-4.710.2238400.1403X-RAY DIFFRACTION
4.71-5.170.2732570.1723X-RAY DIFFRACTION
5.17-5.910.2678570.2119X-RAY DIFFRACTION
5.91-7.380.32530.2081X-RAY DIFFRACTION
7.38-200.2043660.1626X-RAY DIFFRACTION
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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