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- PDB-3lts: Crystal structure of the mutant V182A,I199A of orotidine 5'-monop... -

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Basic information

Entry
Database: PDB / ID: 3lts
TitleCrystal structure of the mutant V182A,I199A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / mutant V182A / I199A / inhibitor BMP / 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 / MOLECULAR REPLACEMENT / Resolution: 1.428 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2010
Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.
Authors: Wood, B.M. / Amyes, T.L. / Fedorov, A.A. / Fedorov, E.V. / Shabila, A. / Almo, S.C. / Richard, J.P. / Gerlt, J.A.
History
DepositionFeb 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 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

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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)50,3094
Polymers49,6292
Non-polymers6802
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-35 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.535, 56.555, 128.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24814.564 Da / Num. of mol.: 2 / Mutation: V182A,I199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: pyrF, MTH_129 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.1M Bis-Tris, 0.2M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.4→38.185 Å / Num. all: 73591 / Num. obs: 73591 / % possible obs: 95.08 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.081

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LTP

3ltp


Resolution: 1.428→38.185 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 3710 5.04 %RANDOM
Rwork0.2544 ---
all0.258 73591 --
obs0.2558 73591 95.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.099 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 1.428→38.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 44 167 3434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073315
X-RAY DIFFRACTIONf_angle_d1.0794480
X-RAY DIFFRACTIONf_dihedral_angle_d19.9861282
X-RAY DIFFRACTIONf_chiral_restr0.074508
X-RAY DIFFRACTIONf_plane_restr0.005589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.428-1.44610.3492470.368972X-RAY DIFFRACTION36
1.4461-1.46510.4284670.36661560X-RAY DIFFRACTION58
1.4651-1.48520.33681020.3462141X-RAY DIFFRACTION79
1.4852-1.50640.37061240.3152513X-RAY DIFFRACTION94
1.5064-1.52890.38811600.29762697X-RAY DIFFRACTION99
1.5289-1.55280.28881340.27772630X-RAY DIFFRACTION100
1.5528-1.57820.29711510.25452711X-RAY DIFFRACTION100
1.5782-1.60550.25461500.24372667X-RAY DIFFRACTION100
1.6055-1.63470.30471260.23352719X-RAY DIFFRACTION100
1.6347-1.66610.24731490.23532722X-RAY DIFFRACTION100
1.6661-1.70010.28371610.2212653X-RAY DIFFRACTION100
1.7001-1.73710.29231310.22652729X-RAY DIFFRACTION100
1.7371-1.77750.26751570.22742671X-RAY DIFFRACTION100
1.7775-1.82190.25981400.2192727X-RAY DIFFRACTION100
1.8219-1.87120.25071420.22342685X-RAY DIFFRACTION100
1.8712-1.92630.27311530.22582696X-RAY DIFFRACTION100
1.9263-1.98840.2461300.21782719X-RAY DIFFRACTION100
1.9884-2.05950.28731510.23152711X-RAY DIFFRACTION100
2.0595-2.14190.26651540.2282722X-RAY DIFFRACTION100
2.1419-2.23940.26681420.23562724X-RAY DIFFRACTION100
2.2394-2.35750.28561530.23132738X-RAY DIFFRACTION100
2.3575-2.50510.28661500.24752722X-RAY DIFFRACTION100
2.5051-2.69850.26421460.26222761X-RAY DIFFRACTION100
2.6985-2.970.24511370.25682765X-RAY DIFFRACTION100
2.97-3.39950.31951550.27042757X-RAY DIFFRACTION100
3.3995-4.28210.2681460.24492822X-RAY DIFFRACTION100
4.2821-38.19880.25651520.26672947X-RAY DIFFRACTION100

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