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- PDB-3ru6: 1.8 Angstrom resolution crystal structure of orotidine 5'-phospha... -

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Entry
Database: PDB / ID: 3ru6
Title1.8 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase (pyrF) from Campylobacter jejuni subsp. jejuni NCTC 11168
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases (CSGID) / TIM-barrel / orotidine 5'-phosphate to UMP and carbon dioxide conversion
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, 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
IODIDE ION / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHalavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.8 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase (pyrF) from Campylobacter jejuni subsp. jejuni NCTC 11168
Authors: Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)143,93434
Polymers140,4934
Non-polymers3,44130
Water9,890549
1
A: Orotidine 5'-phosphate decarboxylase
D: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,84016
Polymers70,2472
Non-polymers1,59414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-45 kcal/mol
Surface area18530 Å2
MethodPISA
2
B: Orotidine 5'-phosphate decarboxylase
C: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,09418
Polymers70,2472
Non-polymers1,84816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-48 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.598, 108.308, 97.707
Angle α, β, γ (deg.)90.00, 95.73, 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: 35123.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj0381c, pyrF / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/magic
References: UniProt: Q9PIC1, orotidine-5'-phosphate decarboxylase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALTHOUGH PROTEIN APPEARS FULL-LENGTH IN SDS GEL ANALYSIS PRIOR TO CRYSTALLIZATION, WE OBSERVE A ...ALTHOUGH PROTEIN APPEARS FULL-LENGTH IN SDS GEL ANALYSIS PRIOR TO CRYSTALLIZATION, WE OBSERVE A TRUNCATED VERSION OF THE PROTEIN, RESIDUES 1 THROUGH 226(227), PERHAPS DUE TO PROTEASE CONTAMINATION. IF THE C-TERMINAL REGION (AND/OR THE N-TERMINAL TAG) IS ABSENT, RATHER THAN DISORDERED, THE MATTHEWS COEFFICIENT (VM) WOULD RISE INTO AN ACCEPTABLE RANGE, WHICH IS 2.35 WITH SOLVENT CONTENT OF 47.65.

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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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 7.3 mg/mL in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Crystallization condition: The PACT suite (F3 (63): 0.2 M Sodium iodide, 0.1 M Bis Tris propane pH 6.5, 20 % w/v PEG3350). ...Details: Protein: 7.3 mg/mL in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Crystallization condition: The PACT suite (F3 (63): 0.2 M Sodium iodide, 0.1 M Bis Tris propane pH 6.5, 20 % w/v PEG3350). Mixed 1:1 v/v , 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: Apr 21, 2011 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond[111] / 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: 84340 / Num. obs: 84340 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.41
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 1.86 / Num. unique all: 4147 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: balbes

Resolution: 1.8→29.12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.671 / SU ML: 0.079 / Isotropic thermal model: istropic / Cross valid method: THROUGHOUT / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20267 4208 5 %RANDOM
Rwork0.16837 ---
obs0.17005 79775 98.41 %-
all-79775 --
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: 32.773 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0.69 Å2
2--0.55 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6993 0 30 549 7572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227515
X-RAY DIFFRACTIONr_bond_other_d0.0010.025267
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.97810146
X-RAY DIFFRACTIONr_angle_other_deg0.862312959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9065953
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.55924.862327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.077151497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.6031538
X-RAY DIFFRACTIONr_chiral_restr0.1040.21147
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028334
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021472
X-RAY DIFFRACTIONr_mcbond_it0.6311.54629
X-RAY DIFFRACTIONr_mcbond_other0.1761.51852
X-RAY DIFFRACTIONr_mcangle_it1.20227532
X-RAY DIFFRACTIONr_scbond_it2.08732886
X-RAY DIFFRACTIONr_scangle_it3.4994.52614
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 300 -
Rwork0.235 5825 -
obs-5825 97.53 %
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)
11.49020.13510.50280.5821-0.17641.39870.07980.13650.0489-0.01190.0127-0.0456-0.02040.1099-0.09250.08470.00820.0270.0635-0.04530.06591.2451-3.037946.7792
23.71280.30980.71161.27040.40941.80750.090.0910.52520.0012-0.07430.0686-0.2377-0.0936-0.01570.10580.02380.07130.02570.01810.11-8.93838.1244.0086
32.0059-0.0299-0.38560.8008-0.13391.315-0.0327-0.2211-0.07240.0320.0425-0.03650.03850.0977-0.00980.0920.0015-0.00060.0723-0.01870.028.248417.43372.3506
45.6314-1.3379-1.12411.60790.64642.3556-0.0891-0.0506-0.70530.0602-0.04780.23270.2887-0.23550.13690.1358-0.04730.0070.07570.04480.1255-3.93816.38445.1509
51.85030.2855-0.05561.59060.02920.75620.00690.00620.2462-0.0392-0.00680.0178-0.0294-0.0253-0.00010.08930.0005-0.00030.0572-0.0260.046410.954732.3488-9.9279
64.80461.02532.14841.4210.82442.5370.01460.44070.1754-0.23030.0907-0.22950.02710.3085-0.10540.10040.01580.04590.09440.03110.091522.470836.9774-20.2207
72.7591-0.39930.03341.3889-0.06160.60290.1639-0.1444-0.51160.0688-0.0903-0.00650.0398-0.0355-0.07350.0964-0.0163-0.04220.0573-0.0070.16154.6498-17.299259.1703
85.6365-1.327-1.97481.58770.97781.93010.0038-0.8063-0.63050.2623-0.0005-0.05350.02710.2422-0.00330.1171-0.0681-0.07290.18860.17120.195714.2958-20.379970.211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 144
2X-RAY DIFFRACTION2A145 - 227
3X-RAY DIFFRACTION3B0 - 150
4X-RAY DIFFRACTION4B151 - 227
5X-RAY DIFFRACTION5C1 - 149
6X-RAY DIFFRACTION6C150 - 227
7X-RAY DIFFRACTION7D1 - 142
8X-RAY DIFFRACTION8D143 - 226

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