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- PDB-4lam: Crystal structure of Cordyceps militaris IDCase D323N mutant in c... -

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Basic information

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


carboxy-lyase activity / hydrolase activity / metal ion binding
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
Chem-5CU / Uracil-5-carboxylate decarboxylase
Similarity search - Component
Biological speciesCordyceps militaris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXu, S. / Li, W. / Zhu, J. / 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

Downloads & links

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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)83,01210
Polymers81,4402
Non-polymers1,5728
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-37 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.361, 77.361, 134.421
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: Chemical ChemComp-5CU / 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 289 K / Method: sitting drop / pH: 8.5
Details: 25% polyethylene glycol 3350, 0.2M MgCl2, 0.1M 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: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 46222 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.085 / Χ2: 1.301 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.183.80.23245731.0321100
2.18-2.263.80.18746201.1671100
2.26-2.373.80.15946261.1781100
2.37-2.493.80.13346051.31100
2.49-2.653.80.11246151.2731100
2.65-2.853.80.09246201.3991100
2.85-3.143.80.0846331.2161100
3.14-3.593.80.07746111.509199.9
3.59-4.523.80.08846261.568199.8
4.52-503.70.05846931.371199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
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: 2.1→38.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.869 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2340 5.1 %RANDOM
Rwork0.1593 ---
obs0.1609 46175 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.31 Å2 / Biso mean: 32.6788 Å2 / Biso min: 10.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 0 70 280 5940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195794
X-RAY DIFFRACTIONr_bond_other_d0.0010.025646
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9797866
X-RAY DIFFRACTIONr_angle_other_deg1.468312992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9975727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40523.216227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42515909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0771534
X-RAY DIFFRACTIONr_chiral_restr0.0620.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216444
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021278
X-RAY DIFFRACTIONr_mcbond_it1.5273.0932923
X-RAY DIFFRACTIONr_mcbond_other1.5273.0922922
X-RAY DIFFRACTIONr_mcangle_it1.5244.6153645
X-RAY DIFFRACTIONr_rigid_bond_restr2.448311436
X-RAY DIFFRACTIONr_sphericity_free16.45563
X-RAY DIFFRACTIONr_sphericity_bonded11.391511519
LS refinement shellResolution: 2.095→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 184 -
Rwork0.181 3164 -
all-3348 -
obs--96.9 %
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)
10.00240.0079-0.02270.0762-0.0850.2190.00040.0012-0.0003-0.0085-0.0015-0.005-0.0036-0.01460.00110.00360.0003-0.00140.0096-0.00220.009795.2945-32.9429-3.945
20.13750.01280.01560.0021-00.0050.0080.00360.00010.0027-0.00510.00020.00020.0075-0.00290.0101-0.00140.00080.0156-0.00140.003563.5288-35.57952.1473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 376
2X-RAY DIFFRACTION2B6 - 374

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