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- PDB-4n2y: Crystal structure of orotidine 5'-monophosphate decarboxylase fro... -

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Basic information

Entry
Database: PDB / ID: 4n2y
TitleCrystal structure of orotidine 5'-monophosphate decarboxylase from Archaeoglobus fulgidus
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / tim barrel
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
Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 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 Archaeoglobus fulgidus
Authors: Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references / Structure summary
Revision 1.2Sep 20, 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0635
Polymers98,9714
Non-polymers921
Water9,116506
1
A: Orotidine 5'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5783
Polymers49,4862
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-32 kcal/mol
Surface area15910 Å2
MethodPISA
2
C: Orotidine 5'-phosphate decarboxylase

D: Orotidine 5'-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)49,4862
Polymers49,4862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y+1/2,-z+31
Buried area3060 Å2
ΔGint-31 kcal/mol
Surface area15830 Å2
MethodPISA
3
A: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8352
Polymers24,7431
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Orotidine 5'-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)24,7431
Polymers24,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Orotidine 5'-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)24,7431
Polymers24,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Orotidine 5'-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)24,7431
Polymers24,7431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.563, 116.859, 87.147
Angle α, β, γ (deg.)90.00, 90.12, 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: 24742.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: pyrF, AF_0929 / Production host: Escherichia coli (E. coli)
References: UniProt: O29333, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PG monomethyl ether 2000,0.1M Tris, 0.01M Ni chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.549→36.563 Å / Num. all: 105168 / Num. obs: 105168 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MUZ

4muz


Resolution: 1.549→36.563 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 3160 3 %
Rwork0.1842 --
obs0.1849 105168 99.3 %
all-105168 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.549→36.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6175 0 6 506 6687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076370
X-RAY DIFFRACTIONf_angle_d1.0378566
X-RAY DIFFRACTIONf_dihedral_angle_d12.9872447
X-RAY DIFFRACTIONf_chiral_restr0.071993
X-RAY DIFFRACTIONf_plane_restr0.0051100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5492-1.57230.31361330.27694198X-RAY DIFFRACTION94
1.5723-1.59690.31391430.26024444X-RAY DIFFRACTION100
1.5969-1.6230.29851170.24544435X-RAY DIFFRACTION100
1.623-1.6510.27111410.23374492X-RAY DIFFRACTION100
1.651-1.68110.2581420.22594420X-RAY DIFFRACTION100
1.6811-1.71340.25321480.20994393X-RAY DIFFRACTION100
1.7134-1.74840.25881530.22364540X-RAY DIFFRACTION100
1.7484-1.78640.29161010.22644375X-RAY DIFFRACTION100
1.7864-1.82790.28411330.21334544X-RAY DIFFRACTION100
1.8279-1.87360.22261350.20654374X-RAY DIFFRACTION100
1.8736-1.92430.23711180.20484524X-RAY DIFFRACTION100
1.9243-1.98090.23821380.19294385X-RAY DIFFRACTION99
1.9809-2.04490.22141360.18554429X-RAY DIFFRACTION99
2.0449-2.11790.20111510.18094449X-RAY DIFFRACTION100
2.1179-2.20270.1881240.16964423X-RAY DIFFRACTION99
2.2027-2.3030.17761360.17734475X-RAY DIFFRACTION100
2.303-2.42430.19771400.18754467X-RAY DIFFRACTION100
2.4243-2.57620.22241500.18334404X-RAY DIFFRACTION100
2.5762-2.7750.1831470.18584477X-RAY DIFFRACTION100
2.775-3.05420.19361460.18344466X-RAY DIFFRACTION100
3.0542-3.49580.22611280.18264443X-RAY DIFFRACTION99
3.4958-4.40320.18631440.15534418X-RAY DIFFRACTION99
4.4032-36.57310.18861560.17134433X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5850.00440.11891.42650.12850.7250.00060.0291-0.0228-0.1232-0.00040.01470.03190.018100.11610.0055-0.00860.1375-0.00280.124431.077211.745675.268
20.46740.17230.22841.2340.7890.8268-0.0097-0.05280.0842-0.0463-0.08120.1556-0.1293-0.0403-0.00130.14850.0001-0.00760.1449-0.01040.159531.835935.384488.9818
30.343-0.0915-0.22461.17840.80310.8435-0.00920.0296-0.06660.0498-0.07180.11890.1343-0.0239-0.00160.13570.0020.00620.1389-0.00550.148913.336937.4307129.0362
40.4048-0.0134-0.18471.1378-0.17450.78450.00260.02820.0276-0.0986-0.00420.0062-0.0244-0.0189-00.12610.00670.00580.1510.00420.133722.98272.3881119.0678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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