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- PDB-3tfx: Crystal structure of Orotidine 5'-phosphate decarboxylase from La... -

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Basic information

Entry
Database: PDB / ID: 3tfx
TitleCrystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / PSI-Biology / NYSGRC / 000529 / Structural Genomics / New York Structural Genomics Research Consortium / TIM barrel fold / Pyrimidine metabolism / UMP biosynthesis via de novo pathway / UMP from orotate / Decarboxylase Lyase
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
Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsSatyanarayana, L. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Satyanarayana, L. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus
Authors: Satyanarayana, L. / Almo, S.C. / Swaminathan, S.
History
DepositionAug 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)57,7362
Polymers57,7362
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-21 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.396, 68.170, 63.930
Angle α, β, γ (deg.)90.00, 106.31, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 240
2114B2 - 240

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Components

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


Mass: 28867.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Top 10 cells (Invitrogen) / Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: LBA1386, pyrF, pyrF/LBA1386 / Plasmid details: T7 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon + RIL
References: UniProt: Q5FJB3, orotidine-5'-phosphate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v 1,6-Hexanediol, 0.2M MgCl2 and 20% w/v Polyethylene glycol 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2010 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 27429 / Num. obs: 27429 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 21.4
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.122 / Num. unique all: 2716 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELX& Arp/Warpmodel building
REFMAC5.5.0109refinement
DENZOdata reduction
HKL-2000data scaling
SHELX& Arp/Warpphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.882 / SU B: 5.45 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25186 1360 5 %RANDOM
Rwork0.20487 ---
obs0.20726 26005 98.43 %-
all-26005 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.602 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å2-0.54 Å2
2--0.26 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 0 283 3744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9854762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.07725.639133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50915640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3161510
X-RAY DIFFRACTIONr_chiral_restr0.0970.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212561
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6041.52261
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17523642
X-RAY DIFFRACTIONr_scbond_it2.20731260
X-RAY DIFFRACTIONr_scangle_it3.474.51120
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1699 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.510.5
medium thermal1.242
LS refinement shellResolution: 2.192→2.248 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 88 -
Rwork0.205 1694 -
obs--87.18 %

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