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- PDB-4df1: Crystal structure of orotidine 5'-monophosphate decarboxylase fro... -

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Basic information

Entry
Database: PDB / ID: 4df1
TitleCrystal structure of orotidine 5'-monophosphate decarboxylase from Thermoproteus neutrophilus complexed with inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE/LYASE inhibitor / TIM barrel / orotidine 5'-monophosphate decarboxylase / inhibitor BMP / LYASE-LYASE inhibitor complex
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
Similarity search - Function
Orotidine 5'-phosphate decarboxylase / 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 / NICKEL (II) ION / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesThermoproteus neutrophilus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of orotidine 5'-monophosphate decarboxylase from Thermoproteus neutrophilus complexed with inhibitor BMP
Authors: Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C.
History
DepositionJan 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)44,7036
Polymers43,9052
Non-polymers7984
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-58 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.158, 62.071, 72.712
Angle α, β, γ (deg.)90.00, 97.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Orotidine 5'-phosphate decarboxylase


Mass: 21952.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus neutrophilus (archaea) / Strain: DSM 2338 / JCM 9278 / V24Sta / Gene: Tneu_0023 / Production host: Escherichia coli (E. coli) / References: UniProt: B1Y9Q9
#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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.1M Sodium citrate, 0.2M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.899→37.348 Å / Num. all: 31340 / Num. obs: 31340 / % possible obs: 95.04 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DF0

4df0


Resolution: 1.899→37.348 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 16.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1791 1578 5.04 %RANDOM
Rwork0.1496 ---
all0.1511 31340 --
obs0.1511 31340 95.04 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.358 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2994 Å2-0 Å2-0.6122 Å2
2---0.3985 Å20 Å2
3---0.0991 Å2
Refinement stepCycle: LAST / Resolution: 1.899→37.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 46 323 3423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073186
X-RAY DIFFRACTIONf_angle_d1.0844343
X-RAY DIFFRACTIONf_dihedral_angle_d13.0931219
X-RAY DIFFRACTIONf_chiral_restr0.072493
X-RAY DIFFRACTIONf_plane_restr0.005558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8995-1.96080.27421070.20931858X-RAY DIFFRACTION66
1.9608-2.03080.17111110.13682573X-RAY DIFFRACTION90
2.0308-2.11210.17111500.13212721X-RAY DIFFRACTION97
2.1121-2.20830.16441600.12792767X-RAY DIFFRACTION97
2.2083-2.32470.17311370.13392803X-RAY DIFFRACTION98
2.3247-2.47030.18031410.14312802X-RAY DIFFRACTION98
2.4703-2.6610.20911520.162807X-RAY DIFFRACTION99
2.661-2.92870.19961510.16192838X-RAY DIFFRACTION99
2.9287-3.35220.1821440.15852850X-RAY DIFFRACTION100
3.3522-4.22250.16141550.1442843X-RAY DIFFRACTION100
4.2225-37.35480.16531700.15352900X-RAY DIFFRACTION99

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