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- PDB-3sy5: Crystal structure of the mutant S127A of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3sy5
TitleCrystal structure of the mutant S127A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor 6azaUMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE/INHIBITOR / tim barrel / 6azaUMP / 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 / 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-AZA URIDINE 5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.321 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Desai, B. / Iiams, V. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the mutant S127A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor 6azaUMP
Authors: Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Iiams, V. / Gerlt, J.A. / Almo, S.C.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Other
Revision 1.2Sep 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 / 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

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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)50,3884
Polymers49,7372
Non-polymers6502
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-42 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.711, 63.603, 61.197
Angle α, β, γ (deg.)90.00, 115.19, 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: 24868.697 Da / Num. of mol.: 2 / Mutation: S127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Strain: Delta H / Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-UP6 / 6-AZA URIDINE 5'-MONOPHOSPHATE / 6-AZA-UMP


Mass: 325.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N3O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 30% PEG 400, 0.1M Hepes, 0.2M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K, pH 7.2

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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: Jul 9, 2011
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: 1.321→29.785 Å / Num. all: 96918 / Num. obs: 96918 / % possible obs: 99.79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PB entry 3G1A

3g1a


Resolution: 1.321→29.785 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 4848 5 %RANDOM
Rwork0.1957 ---
all0.1969 96918 --
obs0.1969 96918 99.79 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.439 Å2 / ksol: 0.405 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0659 Å2-0 Å2-1.0869 Å2
2--1.9599 Å20 Å2
3---0.106 Å2
Refinement stepCycle: LAST / Resolution: 1.321→29.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 42 405 3775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063540
X-RAY DIFFRACTIONf_angle_d1.0394806
X-RAY DIFFRACTIONf_dihedral_angle_d17.6461415
X-RAY DIFFRACTIONf_chiral_restr0.069547
X-RAY DIFFRACTIONf_plane_restr0.007631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.321-1.33550.29831660.28532898X-RAY DIFFRACTION95
1.3355-1.35120.31961680.2783043X-RAY DIFFRACTION100
1.3512-1.36770.28921490.2713050X-RAY DIFFRACTION100
1.3677-1.3850.27381420.25273097X-RAY DIFFRACTION100
1.385-1.40320.26931690.25323025X-RAY DIFFRACTION100
1.4032-1.42250.31431590.2443092X-RAY DIFFRACTION100
1.4225-1.44280.28951610.23273078X-RAY DIFFRACTION100
1.4428-1.46430.25281760.21973029X-RAY DIFFRACTION100
1.4643-1.48720.22631780.20663056X-RAY DIFFRACTION100
1.4872-1.51160.20731570.19983050X-RAY DIFFRACTION100
1.5116-1.53760.2181480.19763092X-RAY DIFFRACTION100
1.5376-1.56560.22611750.18923054X-RAY DIFFRACTION100
1.5656-1.59570.20331560.1943054X-RAY DIFFRACTION100
1.5957-1.62830.21751540.18593069X-RAY DIFFRACTION100
1.6283-1.66370.21771620.18363101X-RAY DIFFRACTION100
1.6637-1.70240.1871460.17923082X-RAY DIFFRACTION100
1.7024-1.74490.17681650.18273075X-RAY DIFFRACTION100
1.7449-1.79210.20451830.18373019X-RAY DIFFRACTION100
1.7921-1.84480.1961660.18623070X-RAY DIFFRACTION100
1.8448-1.90440.22631410.18743104X-RAY DIFFRACTION100
1.9044-1.97240.20991530.18623082X-RAY DIFFRACTION100
1.9724-2.05140.231550.19393081X-RAY DIFFRACTION100
2.0514-2.14470.22331870.19993035X-RAY DIFFRACTION100
2.1447-2.25780.20511700.19713083X-RAY DIFFRACTION100
2.2578-2.39920.22831620.19763084X-RAY DIFFRACTION100
2.3992-2.58430.21481460.2013096X-RAY DIFFRACTION100
2.5843-2.84420.23651730.21043095X-RAY DIFFRACTION100
2.8442-3.25530.20891480.19773112X-RAY DIFFRACTION100
3.2553-4.09970.2051580.1663119X-RAY DIFFRACTION100
4.0997-29.79270.18821750.17693145X-RAY DIFFRACTION99

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