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- PDB-2zz1: Snapshot of the reaction from 6-CN-UMP to BMP catalyzed by Orotid... -

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Basic information

Entry
Database: PDB / ID: 2zz1
TitleSnapshot of the reaction from 6-CN-UMP to BMP catalyzed by Orotidine Monophosphate Deacarboxylase from M. thermoautotrophicum
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE (ODCASE) / BARBITURIC ACID RIBOSYL 5'-MONOPHOSPHATE (BMP) / 6-CYANOUMP OMP decarboxylase / 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-cyanouridine 5'-phosphate / 6-HYDROXYURIDINE-5'-PHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.57 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 / Refinement description / Version format compliance
Revision 1.2Nov 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 1.3Nov 1, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,50610
Polymers54,7592
Non-polymers1,7478
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-50 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.024, 73.543, 59.331
Angle α, β, γ (deg.)90.00, 119.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Orotidine 5'-phosphate decarboxylase / OMP decarboxylase / OMPDCase / OMPdecase


Mass: 27379.402 Da / Num. of mol.: 2 / Mutation: R226L,I227N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: PET15B / 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.: 2 / Source method: obtained synthetically / Formula: C9H13N2O10P
#3: Chemical ChemComp-6CN / 6-cyanouridine 5'-phosphate


Mass: 349.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N3O9P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBMP 301(302) AND 6CN 303(304) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.
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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growMethod: vapor diffusion
Details: 1.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION
PH range: 6.0-8.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2003 / Details: default
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.57→100 Å / Num. obs: 60802 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.06 / Net I/σ(I): 22.1
Reflection shellResolution: 1.57→1.6 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.296 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1x1z

1x1z


Resolution: 1.57→51.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.465 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18249 2979 4.9 %same flag with 1x1z
Rwork0.15551 ---
obs0.15685 57489 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å2-0.33 Å2
2--0.26 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.57→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 114 287 3661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223547
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.67724799
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.485449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44823.333156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00415610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7241536
X-RAY DIFFRACTIONr_chiral_restr0.1140.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022656
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21837
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22419
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1331.52294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72823586
X-RAY DIFFRACTIONr_scbond_it2.9831384
X-RAY DIFFRACTIONr_scangle_it4.8544.51213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 222 -
Rwork0.165 4215 -
obs--99.62 %
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)
10.1697-0.02540.02260.1315-0.03750.29090.00720.0197-0.0141-0.0291-0.01450.00170.0533-0.00110.0073-0.00140.00550.0005-0.01020.0015-0.008124.8057-24.881614.6731
20.17870.0234-0.02190.1322-0.02320.290.01-0.01850.01380.0285-0.01580.0019-0.05330.00120.0058-0.0018-0.00610.0048-0.01050.0028-0.007424.7937-10.504337.078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 225
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A402 - 413
4X-RAY DIFFRACTION1B401 - 414
5X-RAY DIFFRACTION1A461
6X-RAY DIFFRACTION2B11 - 225
7X-RAY DIFFRACTION2B302
8X-RAY DIFFRACTION2A421 - 434
9X-RAY DIFFRACTION2B422 - 433
10X-RAY DIFFRACTION2B462

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