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- PDB-4lan: Crystal structure of Cordyceps militaris IDCase H195A mutant -

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Basic information

Entry
Database: PDB / ID: 4lan
TitleCrystal structure of Cordyceps militaris IDCase H195A mutant
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
Uracil-5-carboxylate decarboxylase
Similarity search - Component
Biological speciesCordyceps militaris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)81,4394
Polymers81,3082
Non-polymers1312
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-127 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.920, 56.440, 105.704
Angle α, β, γ (deg.)90.000, 105.410, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

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Components

#1: Protein Uracil-5-carboxylate decarboxylase


Mass: 40653.883 Da / Num. of mol.: 2 / Mutation: H195A
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.: 589 / 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: 2.56 Å3/Da / Density % sol: 52.01 % / Mosaicity: 0.438 °
Crystal growTemperature: 289 K / Method: sitting drop / pH: 5.6
Details: 30% polyethylene glycol 4000, 0.2M NH4Ac, 0.1M sodium citrate, pH 5.6, sitting drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 82427 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Χ2: 1.264 / Net I/σ(I): 20.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.813.50.29781711.184198.1
1.81-1.893.70.22782351.309199.5
1.89-1.973.70.16482201.343199.6
1.97-2.073.70.12182761.279199.8
2.07-2.23.70.09182791.237199.6
2.2-2.383.80.07282841.22199.5
2.38-2.613.80.0682811.188199.6
2.61-2.993.90.05283161.229199.3
2.99-3.7740.05783451.508199.5
3.77-503.80.03880201.115193.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
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: 1.75→36.32 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.298 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 4097 5 %RANDOM
Rwork0.1556 ---
obs0.1568 82297 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.6 Å2 / Biso mean: 31.1216 Å2 / Biso min: 9.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20.06 Å2
2--2.92 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5633 0 2 589 6224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195787
X-RAY DIFFRACTIONr_bond_other_d0.0010.025618
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.9747888
X-RAY DIFFRACTIONr_angle_other_deg1.511312932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9475741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36323.42231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94415916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8921534
X-RAY DIFFRACTIONr_chiral_restr0.0560.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021271
X-RAY DIFFRACTIONr_rigid_bond_restr3.426311403
X-RAY DIFFRACTIONr_sphericity_free33.6845175
X-RAY DIFFRACTIONr_sphericity_bonded9.499511677
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 310 -
Rwork0.195 5631 -
all-5941 -
obs--97.36 %
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)
10.06180.0482-0.03880.04940.01950.24970.002-0.00410.00750.0015-0.00530.00310.0034-0.00360.00330.0180.0054-0.00170.00240.00060.0312110.913220.009130.0119
20.1850.0019-0.08470.0855-0.01750.0583-0.0088-0.0181-0.0125-0.00220.003-0.0092-0.00140.0070.00580.01310.0061-0.0050.0045-0.00050.0287142.49729.2415123.3331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 374
2X-RAY DIFFRACTION2B5 - 373

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