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- PDB-3g1h: Crystal structure of orotidine 5'-monophosphate decarboxylase fro... -

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Basic information

Entry
Database: PDB / ID: 3g1h
TitleCrystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / orotidine 5'-monophosphate decarboxylase / H2-UMP / 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
5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Chan, K.K. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2009
Title: Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Authors: Chan, K.K. / Wood, B.M. / Fedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Amyes, T.L. / Richard, J.P. / Almo, S.C. / Gerlt, J.A.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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
C: Orotidine 5'-phosphate decarboxylase
D: Orotidine 5'-phosphate decarboxylase
E: Orotidine 5'-phosphate decarboxylase
F: Orotidine 5'-phosphate decarboxylase
G: Orotidine 5'-phosphate decarboxylase
H: Orotidine 5'-phosphate decarboxylase
I: Orotidine 5'-phosphate decarboxylase
J: Orotidine 5'-phosphate decarboxylase
K: Orotidine 5'-phosphate decarboxylase
L: Orotidine 5'-phosphate decarboxylase
M: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,74226
Polymers323,50113
Non-polymers4,24113
Water4,432246
1
A: Orotidine 5'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4224
Polymers49,7692
Non-polymers6522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-44 kcal/mol
Surface area15690 Å2
MethodPISA
2
C: Orotidine 5'-phosphate decarboxylase
D: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4224
Polymers49,7692
Non-polymers6522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-41 kcal/mol
Surface area15370 Å2
MethodPISA
3
E: Orotidine 5'-phosphate decarboxylase
F: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4224
Polymers49,7692
Non-polymers6522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-44 kcal/mol
Surface area15250 Å2
MethodPISA
4
G: Orotidine 5'-phosphate decarboxylase
H: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4224
Polymers49,7692
Non-polymers6522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-42 kcal/mol
Surface area15370 Å2
MethodPISA
5
I: Orotidine 5'-phosphate decarboxylase
J: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4224
Polymers49,7692
Non-polymers6522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-42 kcal/mol
Surface area15540 Å2
MethodPISA
6
K: Orotidine 5'-phosphate decarboxylase
L: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4224
Polymers49,7692
Non-polymers6522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-42 kcal/mol
Surface area15320 Å2
MethodPISA
7
M: Orotidine 5'-phosphate decarboxylase
hetero molecules

M: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4224
Polymers49,7692
Non-polymers6522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area4620 Å2
ΔGint-44 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.897, 101.798, 192.834
Angle α, β, γ (deg.)90.00, 91.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11M-233-

HOH

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Components

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


Mass: 24884.697 Da / Num. of mol.: 13 / Mutation: R101P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical
ChemComp-H2U / 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 326.197 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C9H15N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
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 293K

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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: Mar 21, 2008
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: 2.3→25 Å / Num. all: 126808 / Num. obs: 126808 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G18

3g18


Resolution: 2.3→24.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1916415.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 6367 5 %RANDOM
Rwork0.243 ---
all0.246 126808 --
obs0.243 126808 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8084 Å2 / ksol: 0.331807 e/Å3
Displacement parametersBiso mean: 64 Å2
Baniso -1Baniso -2Baniso -3
1--12.16 Å20 Å2-6.78 Å2
2---0.16 Å20 Å2
3---12.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21358 0 273 246 21877
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d2.7
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.381 633 5 %
Rwork0.364 11911 -
obs-11911 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4H2U_xplor_parH2U_xplor_top
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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