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- PDB-4lal: Crystal structure of Cordyceps militaris IDCase D323A mutant in c... -

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Basic information

Entry
Database: PDB / ID: 4lal
TitleCrystal structure of Cordyceps militaris IDCase D323A 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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
C: Uracil-5-carboxylate decarboxylase
D: Uracil-5-carboxylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,69923
Polymers162,7084
Non-polymers3,99219
Water7,656425
1
A: Uracil-5-carboxylate decarboxylase
B: Uracil-5-carboxylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,20911
Polymers81,3542
Non-polymers1,8559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-45 kcal/mol
Surface area26420 Å2
MethodPISA
2
C: Uracil-5-carboxylate decarboxylase
D: Uracil-5-carboxylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,49112
Polymers81,3542
Non-polymers2,13710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-36 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.266, 54.301, 143.776
Angle α, β, γ (deg.)90.000, 121.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uracil-5-carboxylate decarboxylase


Mass: 40676.941 Da / Num. of mol.: 4 / Mutation: D323A
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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
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: 74453 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.077 / Χ2: 1.203 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.183.50.26773780.97199.5
2.18-2.263.50.23573431.262199.3
2.26-2.373.50.20274241.193199.6
2.37-2.493.60.15973551.245199.8
2.49-2.653.60.13673751.315199.7
2.65-2.853.70.11174891.21199.8
2.85-3.143.70.08574291.138199.8
3.14-3.593.70.07374591.33199.8
3.59-4.523.70.07275441.4371100
4.52-503.60.04376570.917199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HK5

4hk5


Resolution: 2.1→47.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.95 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 3750 5 %RANDOM
Rwork0.1749 ---
obs0.1772 74452 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.62 Å2 / Biso mean: 31.1058 Å2 / Biso min: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å21.69 Å2
2---2.09 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11241 0 176 425 11842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01911687
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211378
X-RAY DIFFRACTIONr_angle_refined_deg1.0171.98215859
X-RAY DIFFRACTIONr_angle_other_deg0.848326196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.99351466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44123.29459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.786151822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9051568
X-RAY DIFFRACTIONr_chiral_restr0.0520.21793
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112990
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022562
X-RAY DIFFRACTIONr_mcbond_it0.9132.9035885
X-RAY DIFFRACTIONr_mcbond_other0.9132.9035884
X-RAY DIFFRACTIONr_mcangle_it1.0544.3497344
X-RAY DIFFRACTIONr_rigid_bond_restr4.173323056
X-RAY DIFFRACTIONr_sphericity_free25.7035108
X-RAY DIFFRACTIONr_sphericity_bonded3.199523103
LS refinement shellResolution: 2.097→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 239 -
Rwork0.187 4797 -
all-5036 -
obs--91.75 %
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)
10.4148-0.0404-0.05510.53290.08720.55420.01460.0282-0.0091-0.0454-0.0089-0.0151-0.02260.0319-0.00570.02130.0077-0.00940.0144-0.01260.0418-27.52229.96856.4956
20.6514-0.0766-0.10270.5003-0.11360.5161-0.0056-0.1208-0.02030.0768-0.00190.0458-0.0527-0.02570.00750.0290.00630.00150.0381-0.01510.0301-42.532614.939834.9864
30.84530.1274-0.32560.7014-0.1590.6532-0.00190.002-0.0419-0.0068-0.0448-0.0634-0.00490.04470.04670.0084-0.00130.0010.01060.01550.03117.28-13.423427.0706
40.6865-0.0027-0.48370.8641-0.06190.77170.0286-0.1945-0.05220.1817-0.03330.0231-0.02240.10140.00460.0535-0.01960.00490.06060.01580.0074-10.2681-17.815154.1426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 373
2X-RAY DIFFRACTION2B6 - 373
3X-RAY DIFFRACTION3C6 - 374
4X-RAY DIFFRACTION4D6 - 374

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