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- PDB-4nx5: Crystal structure of orotidine 5'-monophosphate decarboxylase fro... -

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Basic information

Entry
Database: PDB / ID: 4nx5
TitleCrystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / tim barrel / OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE / 6-AZAURIDINE 5'-MONOPHOSPHATE
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-AZA URIDINE 5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Chan, K.K. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate
Authors: Fedorov, A.A. / Fedorov, E.V. / Chan, K.K. / Gerlt, J.A. / Almo, S.C.
History
DepositionDec 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)50,85613
Polymers49,7692
Non-polymers1,08711
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-102 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.737, 64.148, 61.527
Angle α, β, γ (deg.)90.00, 115.36, 90.00
Int Tables number4
Space group name H-MP1211

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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: 24884.697 Da / Num. of mol.: 2 / Fragment: R101P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase

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Non-polymers , 6 types, 434 molecules

#2: Chemical ChemComp-UP6 / 6-AZA URIDINE 5'-MONOPHOSPHATE / 6-AZA-UMP


Mass: 325.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N3O9P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.1M TRIS, 0.2M MAGNESIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.591→32.406 Å / Num. all: 56307 / Num. obs: 56307 / % possible obs: 99.86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G18

3g18


Resolution: 1.591→32.406 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 16.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.168 1740 3.09 %RANDOM
Rwork0.1477 ---
obs0.1484 56307 99.86 %-
all-56307 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.591→32.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 64 423 3817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073577
X-RAY DIFFRACTIONf_angle_d1.094846
X-RAY DIFFRACTIONf_dihedral_angle_d11.7621355
X-RAY DIFFRACTIONf_chiral_restr0.075544
X-RAY DIFFRACTIONf_plane_restr0.006644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5913-1.63810.17781350.14384481X-RAY DIFFRACTION99
1.6381-1.6910.18841320.14244552X-RAY DIFFRACTION100
1.691-1.75140.15961270.14144581X-RAY DIFFRACTION100
1.7514-1.82160.19291370.14264494X-RAY DIFFRACTION100
1.8216-1.90440.17981190.14324577X-RAY DIFFRACTION100
1.9044-2.00480.16931610.14384526X-RAY DIFFRACTION100
2.0048-2.13040.14431340.14394559X-RAY DIFFRACTION100
2.1304-2.29490.15081750.14484528X-RAY DIFFRACTION100
2.2949-2.52570.19021670.15394512X-RAY DIFFRACTION100
2.5257-2.8910.18731490.16344556X-RAY DIFFRACTION100
2.891-3.64160.16431630.154569X-RAY DIFFRACTION100
3.6416-32.41320.15431410.14314632X-RAY DIFFRACTION99
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)
11.29-0.00310.16390.6918-0.16240.6282-0.02120.05420.07-0.0266-0.0063-0.0576-0.05040.08920.02080.0764-0.00390.01340.04430.00230.06153.08666.435766.3608
21.35660.29410.09840.6704-0.03180.99330.0396-0.1834-0.07980.0538-0.0434-0.0040.055-0.06470.00620.0738-0.00420.00770.05110.01250.062333.7473-7.731978.1271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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