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- PDB-3r89: Crystal structure of orotidine 5-phosphate decarboxylase from Ana... -

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Basic information

Entry
Database: PDB / ID: 3r89
TitleCrystal structure of orotidine 5-phosphate decarboxylase from Anaerococcus prevotii DSM 20548
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / PSI-biology / Midwest center for structural genomics / MCSG / orotidine 5-phosphate decarboxylase
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, type 2 / 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 speciesAnaerococcus prevotii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.844 Å
AuthorsChang, C. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of orotidine 5'-phosphate decarboxylase from Anaerococcus prevotii DSM 20548
Authors: Chang, C. / Tesar, C. / Bearden, J. / Joachimiak, A.
History
DepositionMar 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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


Theoretical massNumber of molelcules
Total (without water)66,6152
Polymers66,6152
Non-polymers00
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-34 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.507, 108.848, 138.171
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33307.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaerococcus prevotii (bacteria) / Strain: ATCC 9321 / DSM 20548 / JCM 6508 / PC1 / Gene: pyrF, Apre_0783 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: C7RH50, orotidine-5'-phosphate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M NaCl, 0.1 M Tris pH 7.0, 30% (w/v) PEG-3000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.844→85.503 Å / Num. all: 52163 / Num. obs: 49114 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 30.7
Reflection shellResolution: 1.844→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2.72 / Num. unique all: 2412 / % possible all: 92.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.844→85.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.707 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2488 5.1 %RANDOM
Rwork0.1584 ---
all0.1604 48644 --
obs0.1604 48644 93.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.93 Å2 / Biso mean: 19.769 Å2 / Biso min: 6.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.844→85.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 0 440 5044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224908
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9746615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03925.042238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70615918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.821521
X-RAY DIFFRACTIONr_chiral_restr0.1040.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023767
X-RAY DIFFRACTIONr_mcbond_it0.7611.52979
X-RAY DIFFRACTIONr_mcangle_it1.37724793
X-RAY DIFFRACTIONr_scbond_it2.56831929
X-RAY DIFFRACTIONr_scangle_it4.2094.51822
LS refinement shellResolution: 1.844→1.892 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 180 -
Rwork0.217 2948 -
all-3128 -
obs-3128 90.04 %
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)
10.18130.07770.22240.1719-0.0850.52380.01810.0230.0008-0.0154-0.00260.00010.07740.0483-0.01550.03890.0078-0.00230.0236-0.010.042330.3296-4.086322.9604
20.1637-0.14260.08580.1467-0.00990.8676-0.01590.02460.0115-0.010.00170.0129-0.10970.09340.01420.0353-0.0312-0.0140.02870.01690.04632.577116.193322.3212
30.36760.3060.27470.6888-0.43061.2121-0.0163-0.04120.0121-0.04350.00670.01490.0159-0.09590.00960.0343-0.0002-0.00210.0481-0.01120.025916.8601-0.89419.1904
40.238-0.06790.23130.11320.08190.46320.0182-0.0146-0.01730.0149-0.00160.00690.0627-0.026-0.01660.0394-0.003-0.00140.0180.00520.044728.5562-4.884348.7896
50.17230.095-0.00150.0583-0.06250.6989-0.0072-0.0268-0.00120.007-0.0063-0.0022-0.0999-0.05150.01360.03790.0214-0.00830.0167-0.0070.040226.356715.315750.4088
60.3451-0.4401-0.06450.95540.69381.06330.01930.00690.03470.06080.0053-0.0620.07740.0712-0.02460.0522-0.0014-0.00340.06590.01080.016142.1382-2.533362.2231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 128
2X-RAY DIFFRACTION2A129 - 248
3X-RAY DIFFRACTION3A249 - 286
4X-RAY DIFFRACTION4B-2 - 128
5X-RAY DIFFRACTION5B129 - 248
6X-RAY DIFFRACTION6B249 - 286

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