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- PDB-2zz7: Orotidine Monophosphate Decarboxylase K72A mutant complexed with ... -

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Basic information

Entry
Database: PDB / ID: 2zz7
TitleOrotidine Monophosphate Decarboxylase K72A mutant complexed with BMP (produced from 6-Iodo-UMP)
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / ODCase / OMPDC / OMPDCase / Decarboxylase / Pyrimidine biosynthesis
Function / homology
Function and homology information


orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol
Similarity search - Function
: / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel ...: / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-HYDROXYURIDINE-5'-PHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.58 Å
AuthorsFujihashi, M. / Pai, E.F.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase
Authors: Fujihashi, M. / Wei, L. / Kotra, L.P. / Pai, E.F.
History
DepositionFeb 5, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8464
Polymers27,3211
Non-polymers5243
Water3,315184
1
A: Orotidine 5'-phosphate decarboxylase
hetero molecules

A: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6918
Polymers54,6432
Non-polymers1,0496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5430 Å2
ΔGint-48 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.933, 103.290, 73.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-451-

HOH

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Components

#1: Protein Orotidine 5'-phosphate decarboxylase / OMP DECARBOXYLASE / OMPDCASE / OMPDECASE


Mass: 27321.299 Da / Num. of mol.: 1 / Mutation: K72A,R226L,I227N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: pET-15b / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-BMP / 6-HYDROXYURIDINE-5'-PHOSPHATE


Type: RNA linking / Mass: 340.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O10P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. ...ACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. DEPOSITORS SEQUENCED THE GENOME FROM M. THERMOAUTOTROPHICUM AND CONFIRMD IT IS PRO.

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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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 1.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION, temperature 298K
PH range: 6.0-8.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.0332 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2004 / Details: default
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.58→200 Å / Num. obs: 30641 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 33.2
Reflection shellResolution: 1.58→1.61 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: ODCase from M. thermoautotrophicum

Resolution: 1.58→51.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.224 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1708 1518 5 %RANDOM
Rwork0.15155 ---
obs0.15251 28996 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2---0.73 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.58→51.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 34 184 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221878
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9952558
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42323.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17315323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8291521
X-RAY DIFFRACTIONr_chiral_restr0.1120.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021449
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2958
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21288
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0351.51217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53821917
X-RAY DIFFRACTIONr_scbond_it2.7813725
X-RAY DIFFRACTIONr_scangle_it4.4764.5641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 90 -
Rwork0.156 2143 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: 18.7778 Å / Origin y: 40.3435 Å / Origin z: 29.5132 Å
111213212223313233
T-0.0043 Å20.0014 Å2-0.0109 Å2--0.0125 Å20.0006 Å2---0.0229 Å2
L0.3397 °2-0.0032 °20.0177 °2-0.5961 °2-0.1205 °2--0.2384 °2
S0.0079 Å °0.0286 Å °-0.0372 Å °-0.0905 Å °0.0124 Å °0.0185 Å °0.0515 Å °0.0087 Å °-0.0203 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 225
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A311 - 475

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