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- PDB-4lak: Crystal structure of Cordyceps militaris IDCase D323N mutant in a... -

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Basic information

Entry
Database: PDB / ID: 4lak
TitleCrystal structure of Cordyceps militaris IDCase D323N mutant in apo form
ComponentsUracil-5-carboxylate decarboxylase
KeywordsLYASE / pyrimidine metabolism / IDCase / decarboxylase / uracil / DNA decarboxylation
Function / homology
Function and homology information


secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Uracil-5-carboxylate decarboxylase
Similarity search - Component
Biological speciesCordyceps militaris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsXu, S. / Li, W. / Zhu, J. / Wang, R. / Li, Z. / Xu, G.L. / Ding, J.
CitationJournal: Cell Res. / Year: 2013
Title: Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase.
Authors: Xu, S. / Li, W. / Zhu, J. / Wang, R. / Li, Z. / Xu, G.L. / Ding, J.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_asym_id / _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_asym_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

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Assembly

Deposited unit
A: Uracil-5-carboxylate decarboxylase
B: Uracil-5-carboxylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5714
Polymers81,4402
Non-polymers1312
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-126 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.618, 77.618, 140.089
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Uracil-5-carboxylate decarboxylase


Mass: 40719.965 Da / Num. of mol.: 2 / Mutation: D323N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cordyceps militaris (fungus) / Strain: CM01 / Gene: CCM_01452 / Plasmid: pET28Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: G3J531
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.59 Å3/Da / Density % sol: 52.52 % / Mosaicity: 0.419 °
Crystal growTemperature: 289 K / Method: sitting drop / pH: 8.5
Details: 25% polyethylene glycol 3350, 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, sitting drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→77.62 Å / Num. obs: 31075 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.103 / Χ2: 1.118 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.493.50.65631250.906198.4
2.49-2.593.50.54531310.941198.2
2.59-2.73.50.37931380.979198.3
2.7-2.853.50.28631261.025197.8
2.85-3.023.50.231171.104197.7
3.02-3.263.50.14331341.07197.6
3.26-3.583.50.09930921.11197.3
3.58-4.13.50.0831201.256196.9
4.1-5.173.50.0730921.401196.2
5.17-503.40.06830001.409192.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HK5

4hk5


Resolution: 2.41→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.232 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 1580 5.1 %RANDOM
Rwork0.1807 ---
obs0.1838 31074 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.53 Å2 / Biso mean: 57.078 Å2 / Biso min: 25.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.41→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5339 0 2 99 5440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195476
X-RAY DIFFRACTIONr_angle_refined_deg0.9751.9687454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2225694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13723.196219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88615865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6011532
X-RAY DIFFRACTIONr_chiral_restr0.0630.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214143
X-RAY DIFFRACTIONr_rigid_bond_restr1.12335476
X-RAY DIFFRACTIONr_sphericity_free29.559539
X-RAY DIFFRACTIONr_sphericity_bonded34.31155401
LS refinement shellResolution: 2.409→2.471 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 113 -
Rwork0.218 2117 -
all-2230 -
obs--96.2 %

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