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- PDB-3uwq: 1.80 Angstrom resolution crystal structure of orotidine 5'-phosph... -

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Basic information

Entry
Database: PDB / ID: 3uwq
Title1.80 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with uridine-5'-monophosphate (UMP)
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / Orotidine 5'-Phosphate Decarboxylase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / Decarboxylase / Pyrimidine biosynthesis / CSGID / uridine-5'-monophosphate / 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 / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / URIDINE-5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHalavaty, A.S. / Minasov, G. / Winsor, J. / Shuvalova, L. / Kuhn, M. / Filippova, E.V. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.80 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with uridine-5'-monophosphate (UMP)
Authors: Halavaty, A.S. / Minasov, G. / Winsor, J. / Shuvalova, L. / Kuhn, M. / Filippova, E.V. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
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

Downloads & links

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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)57,50812
Polymers55,5542
Non-polymers1,95410
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-12 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.140, 96.944, 104.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 27776.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: Vibrio cholerae O1 biovar eltor str. N16961 / Gene: pyrF, VC_1911 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic
References: UniProt: Q9KQT7, orotidine-5'-phosphate decarboxylase

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Non-polymers , 6 types, 478 molecules

#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein at 7 mg/mL in 10 mM Tris-HCl, 500 mM NaCl, 5 mM BME. Crystallization condition: the PACT Suite (A4: 0.1 M SPG buffer pH 7.0 25 % (w/v) PEG1500), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2011 / Details: Be-Lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 49918 / Num. obs: 49918 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 29.48
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2440 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3LDV

3ldv


Resolution: 1.8→29.33 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.034 / SU ML: 0.059 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17787 2516 5.1 %RANDOM
Rwork0.1502 ---
obs0.15158 47123 99.98 %-
all-47123 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.189 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å2-0 Å2
2---1.04 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 129 468 3986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223857
X-RAY DIFFRACTIONr_bond_other_d0.0010.022685
X-RAY DIFFRACTIONr_angle_refined_deg1.6312.0095229
X-RAY DIFFRACTIONr_angle_other_deg0.91736597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.3735500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.90123.907151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.57615671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.6231528
X-RAY DIFFRACTIONr_chiral_restr0.0970.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_mcbond_it0.4891.52403
X-RAY DIFFRACTIONr_mcbond_other0.1211.5961
X-RAY DIFFRACTIONr_mcangle_it0.9423904
X-RAY DIFFRACTIONr_scbond_it1.59831454
X-RAY DIFFRACTIONr_scangle_it2.7364.51325
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 194 -
Rwork0.179 3391 -
obs-3391 100 %
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)
10.6980.31160.20761.28610.35010.7322-0.01820.0052-0.03190.08220.0737-0.11180.00510.0924-0.05550.00860.0088-0.01010.0543-0.0240.028-14.102117.2159-6.0559
20.8782-0.5376-0.01421.64220.4322.55560.01570.0568-0.0453-0.1556-0.05040.1454-0.0549-0.11180.03470.01710.0065-0.01920.061-0.02070.0655-28.831711.6087-17.0718
31.60550.3147-0.14022.7294-0.52161.0386-0.04020.11740.1138-0.07260.0420.0202-0.07120.0136-0.00180.01320.0056-0.0030.06050.01060.0082-29.657826.735-15.418
46.09781.01890.46112.41490.10852.3814-0.18310.04730.35060.04580.0836-0.079-0.44050.13670.09950.1015-0.0274-0.04140.03910.03020.0626-13.734135.4824-9.9219
50.8684-0.37670.15942.08080.15631.40650.0031-0.0501-0.04530.17180.1165-0.27510.11110.1897-0.11970.02250.0271-0.03670.0877-0.05960.0816-6.8432-0.2451-13.6051
62.46550.28920.00342.13370.61141.32120.00310.1095-0.0292-0.36590.0076-0.0599-0.06840.0956-0.01070.09140.0030.00720.0635-0.03550.0265-15.84024.0897-29.1949
70.7914-0.1750.07654.51190.282.2160.0434-0.0154-0.0763-0.02330.1188-0.00830.1985-0.0279-0.16210.0266-0.0039-0.01610.071-0.04290.0504-15.6886-12.7414-27.7588
84.0004-1.5086-0.89433.9340.67066.3987-0.0479-0.2446-0.64070.6130.16540.05740.60640.1418-0.11760.23140.0216-0.10090.0712-0.00280.1841-9.8402-18.6157-12.8667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 87
2X-RAY DIFFRACTION2A88 - 147
3X-RAY DIFFRACTION3A148 - 207
4X-RAY DIFFRACTION4A208 - 230
5X-RAY DIFFRACTION5B3 - 92
6X-RAY DIFFRACTION6B93 - 154
7X-RAY DIFFRACTION7B155 - 207
8X-RAY DIFFRACTION8B208 - 230

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