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- PDB-2zz5: Orotidine Monophosphate Deacarboxylase D70A/K72A double mutant fr... -

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Basic information

Entry
Database: PDB / ID: 2zz5
TitleOrotidine Monophosphate Deacarboxylase D70A/K72A double mutant from M. thermoautotrophicum complexed with 6- cyano-UMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE (ODCASE) / 6-CYANOUMP OMP decarboxylase / OMPDC / OMPDCASE / Decarboxylase / Pyrimidine biosynthesis
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
6-cyanouridine 5'-phosphate / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsFujihashi, M. / Pai, E.F.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase
Authors: Fujihashi, M. / Wei, L. / Kotra, L.P. / Pai, E.F.
History
DepositionFeb 5, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)55,2534
Polymers54,5552
Non-polymers6982
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-35 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.556, 64.359, 61.539
Angle α, β, γ (deg.)90.00, 115.52, 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: 27277.289 Da / Num. of mol.: 2 / Mutation: D70A,K72A,R226L,I227N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-6CN / 6-cyanouridine 5'-phosphate


Mass: 349.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N3O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. ...ACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. DEPOSITORS SEQUENCED THE GENOME FROM M. THERMOAUTOTROPHICUM AND CONFIRMD IT IS PRO.

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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: 1.95 Å3/Da / Density % sol: 36.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 1.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION, temperature 298K
PH range: 6.0-8.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2006 / Details: default
RadiationMonochromator: default / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.56→100 Å / Num. obs: 50081 / % possible obs: 83.9 % / Redundancy: 3.6 % / Rsym value: 0.083 / Net I/σ(I): 9.9
Reflection shellResolution: 1.56→1.59 Å / Mean I/σ(I) obs: 1.4 / Rsym value: 0.43 / % possible all: 30.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E6Y

2e6y


Resolution: 1.56→55.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.468 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18679 2544 5.1 %RANDOM
Rwork0.15976 ---
obs0.16118 47506 83.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-1.05 Å2
2--0.22 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.56→55.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 46 199 3465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223512
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.994771
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.822.821156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49215599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4851540
X-RAY DIFFRACTIONr_chiral_restr0.1280.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022714
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21770
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22493
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2581.52312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85523585
X-RAY DIFFRACTIONr_scbond_it3.32131346
X-RAY DIFFRACTIONr_scangle_it5.3724.51185
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.561→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 64 -
Rwork0.256 1318 -
obs--31.82 %
Refinement TLS params.Method: refined / Origin x: 6.6042 Å / Origin y: -6.9473 Å / Origin z: 11.1448 Å
111213212223313233
T-0.0193 Å2-0.0112 Å2-0.0095 Å2--0.0331 Å20.0079 Å2---0.0213 Å2
L0.7078 °2-0.2812 °2-0.0862 °2-0.2889 °20.1125 °2--0.3463 °2
S0.0082 Å °0.0706 Å °0.0085 Å °-0.0002 Å °-0.036 Å °0.0065 Å °-0.0086 Å °-0.0179 Å °0.0278 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B401 - 664
2X-RAY DIFFRACTION1A402 - 663
3X-RAY DIFFRACTION1B302
4X-RAY DIFFRACTION1A301
5X-RAY DIFFRACTION1B9 - 222
6X-RAY DIFFRACTION1A9 - 221

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