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- PDB-2z2b: Deletion 107-116 mutant of dihydroorotase from E. coli -

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Basic information

Entry
Database: PDB / ID: 2z2b
TitleDeletion 107-116 mutant of dihydroorotase from E. coli
ComponentsDihydroorotase
KeywordsHYDROLASE / TIM barrel
Function / homology
Function and homology information


dihydroorotase / pyrimidine nucleotide biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / protein homodimerization activity / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLee, M. / Maher, M.J. / Guss, J.M.
CitationJournal: Biochemistry / Year: 2007
Title: Kinetic and Structural Analysis of Mutant Escherichia coli Dihydroorotases: A Flexible Loop Stabilizes the Transition State
Authors: Lee, M. / Maher, M.J. / Christopherson, R.I. / Guss, J.M.
History
DepositionMay 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 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 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9323
Polymers37,8011
Non-polymers1312
Water2,450136
1
A: Dihydroorotase
hetero molecules

A: Dihydroorotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8646
Polymers75,6022
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,x-y+1,-z1
Unit cell
Length a, b, c (Å)52.296, 52.296, 215.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-1409-

HOH

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Components

#1: Protein Dihydroorotase / DHOase


Mass: 37801.105 Da / Num. of mol.: 1 / Mutation: Deletion (107-116) mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrC / Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / Strain (production host): X7014a / References: UniProt: P05020, dihydroorotase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 45.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG 3350, 0.1M MES, 75mM MgCl2, 0.15M KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2006
RadiationMonochromator: Double crystal cryocooled Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 28254 / Num. obs: 28254 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.4
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1950 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XGE

1xge


Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.809 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24546 1430 5.1 %RANDOM
Rwork0.19118 ---
obs0.19379 28254 95.9 %-
all-28254 --
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: 51.878 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20 Å2
2---0.11 Å20 Å2
3---0.16 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 2 136 2749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222615
X-RAY DIFFRACTIONr_bond_other_d0.0010.022397
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9613563
X-RAY DIFFRACTIONr_angle_other_deg0.87335534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97823.475118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62815410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0021519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022932
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_nbd_refined0.2140.2539
X-RAY DIFFRACTIONr_nbd_other0.1750.22470
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21303
X-RAY DIFFRACTIONr_nbtor_other0.0840.21526
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.110.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.73842121
X-RAY DIFFRACTIONr_mcbond_other1.6944661
X-RAY DIFFRACTIONr_mcangle_it5.19362665
X-RAY DIFFRACTIONr_scbond_it4.78641087
X-RAY DIFFRACTIONr_scangle_it6.2276898
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 107 -
Rwork0.247 1843 -
obs-1950 91.25 %
Refinement TLS params.Method: refined / Origin x: -6.2346 Å / Origin y: 12.6643 Å / Origin z: 17.7524 Å
111213212223313233
T-0.2223 Å20.0279 Å20.0342 Å2--0.2783 Å20.0188 Å2---0.2649 Å2
L2.1226 °2-1.0354 °21.2208 °2-2.3061 °2-0.6092 °2--3.1508 °2
S-0.2218 Å °-0.074 Å °0.0509 Å °0.2558 Å °0.0139 Å °-0.1009 Å °-0.2329 Å °0.2261 Å °0.2079 Å °

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