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- PDB-4mjz: 2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-... -

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Basic information

Entry
Database: PDB / ID: 4mjz
Title2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-monophosphate-decarboxylase from Toxoplasma gondii.
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / glycosyltransferase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
Orotidine 5'-phosphate decarboxylase, type 2 / 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 ...Orotidine 5'-phosphate decarboxylase, type 2 / 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
NITRATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Orotidine 5'-phosphate decarboxylase / :
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMinasov, G. / Wawrzak, Z. / Ruan, J. / Ngo, H. / Shuvalova, L. / Dubrovska, I. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-monophosphate-decarboxylase from Toxoplasma gondii.
Authors: Minasov, G. / Wawrzak, Z. / Ruan, J. / Ngo, H. / Shuvalova, L. / Dubrovska, I. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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

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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)70,7198
Polymers70,0832
Non-polymers6376
Water1,27971
1
A: Orotidine 5'-phosphate decarboxylase
hetero molecules

A: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8088
Polymers70,0832
Non-polymers7256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area4710 Å2
ΔGint-30 kcal/mol
Surface area22040 Å2
MethodPISA
2
B: Orotidine 5'-phosphate decarboxylase
hetero molecules

B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6318
Polymers70,0832
Non-polymers5486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area4700 Å2
ΔGint-30 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.477, 115.477, 152.055
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

21B-507-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.864995, 0.501716, -0.008048), (-0.501771, -0.864967, 0.007646), (-0.003125, 0.010652, 0.999938)57.83767, 99.94924, 12.59765

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Components

#1: Protein Orotidine 5'-phosphate decarboxylase


Mass: 35041.387 Da / Num. of mol.: 2 / Fragment: UNP residues 12-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGGT1_010340 / Plasmid: pCCK-N'-6XHisTag-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: B9PKU1, UniProt: B6KBH9*PLUS, orotidine-5'-phosphate decarboxylase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: Protein: 7.7 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, 0.02M Magnesium chloride, 0.02M UMP Screen: JCSG+(C3), 0.2M Ammonium nitrate pH 6.3, 20% (w/v) PEG 3350, VAPOR ...Details: Protein: 7.7 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, 0.02M Magnesium chloride, 0.02M UMP Screen: JCSG+(C3), 0.2M Ammonium nitrate pH 6.3, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2013 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 16220 / Num. obs: 16220 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 53.3 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 24.2
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 5.3 / Num. unique all: 797 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QW4

3qw4


Resolution: 2.75→29.1 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 27.675 / SU ML: 0.265
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24602 809 5 %RANDOM
Rwork0.18817 ---
all0.19092 15330 --
obs0.19092 15330 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.175 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.77 Å2-0 Å2
2--1.55 Å2-0 Å2
3----5.02 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4381 0 42 71 4494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194529
X-RAY DIFFRACTIONr_bond_other_d0.0050.024349
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9776125
X-RAY DIFFRACTIONr_angle_other_deg1.39439991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.1825584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.30423.805205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49715728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7941540
X-RAY DIFFRACTIONr_chiral_restr0.0820.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215230
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021022
X-RAY DIFFRACTIONr_mcbond_it2.0232.8542336
X-RAY DIFFRACTIONr_mcbond_other2.0122.8532335
X-RAY DIFFRACTIONr_mcangle_it3.3734.2742920
X-RAY DIFFRACTIONr_mcangle_other3.3724.2762921
X-RAY DIFFRACTIONr_scbond_it2.5923.2082189
X-RAY DIFFRACTIONr_scbond_other2.5893.2082189
X-RAY DIFFRACTIONr_scangle_other4.1654.6563206
X-RAY DIFFRACTIONr_long_range_B_refined6.3922.725048
X-RAY DIFFRACTIONr_long_range_B_other6.38922.7285048
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 64 -
Rwork0.254 1088 -
obs-1088 99.91 %
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)
11.1512-0.5269-0.77991.56921.26893.5729-0.13970.16790.1369-0.10690.0637-0.0311-0.03020.12940.0760.1027-0.0542-0.00120.05250.03220.073151.65871.758515.3623
21.2150.2068-0.96021.89090.2032.1679-0.21080.115-0.3229-0.1083-0.03610.18120.4032-0.20320.24690.231-0.09030.04460.0798-0.02350.149543.191955.793511.6114
30.9142-0.2371-0.27771.8157-1.32782.9789-0.02040.1287-0.1148-0.12150.05410.0322-0.0184-0.2212-0.03370.049-0.027-0.00880.063-0.03460.135219.711721.37662.8089
41.25450.45970.61711.7912-0.42711.8871-0.13750.02690.0626-0.0913-0.0519-0.417-0.24120.25620.18940.0929-0.0786-0.00780.08160.02380.216734.68230.7286-1.0773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 138
2X-RAY DIFFRACTION2A139 - 318
3X-RAY DIFFRACTION3B21 - 140
4X-RAY DIFFRACTION4B141 - 316

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