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- PDB-4lao: Crystal structure of Cordyceps militaris IDCase H195A mutant (Zn) -

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Basic information

Entry
Database: PDB / ID: 4lao
TitleCrystal structure of Cordyceps militaris IDCase H195A mutant (Zn)
ComponentsCordyceps militaris IDCase
KeywordsLYASE / pyrimidine metabolism / IDCase / decarboxylase / uracil / DNA decarboxylation
Function / homology
Function and homology information


organic substance metabolic process / 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
DI(HYDROXYETHYL)ETHER / Uracil-5-carboxylate decarboxylase
Similarity search - Component
Biological speciesCordyceps militaris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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Assembly

Deposited unit
A: Cordyceps militaris IDCase
B: Cordyceps militaris IDCase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5455
Polymers81,3082
Non-polymers2373
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-120 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.365, 57.510, 105.563
Angle α, β, γ (deg.)90.000, 105.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-524-

HOH

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Components

#1: Protein Cordyceps militaris IDCase


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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.6 Å3/Da / Density % sol: 52.68 % / Mosaicity: 0.596 °
Crystal growTemperature: 289 K / Method: sitting drop / pH: 5.6
Details: 30% polyethylene glycol 4000, 0.2M NH4Ac, 2mM ZnCl2, 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: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 55498 / % possible obs: 97.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.062 / Χ2: 1.042 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.074.20.35554380.943197.1
2.07-2.154.30.26954860.992197.5
2.15-2.254.30.2154831.137197.5
2.25-2.374.30.17455041.1197.7
2.37-2.524.30.13955471.14198
2.52-2.714.20.10755561.025198.1
2.71-2.994.20.07755821.008198.4
2.99-3.424.20.05955951.078198.6
3.42-4.314.10.0456291.063198.7
4.31-5040.03156780.924197.3

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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→45.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.809 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 2824 5.1 %RANDOM
Rwork0.1685 ---
obs0.1704 55498 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.27 Å2 / Biso mean: 38.0096 Å2 / Biso min: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å2-0 Å2-0.19 Å2
2--4.09 Å2-0 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5633 0 9 393 6035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195781
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.9757874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7065737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85423.391230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33615912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5911534
X-RAY DIFFRACTIONr_chiral_restr0.0680.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214380
X-RAY DIFFRACTIONr_mcbond_it1.1593.6322954
X-RAY DIFFRACTIONr_mcangle_it1.1835.4393689
X-RAY DIFFRACTIONr_scbond_it1.4793.8562826
X-RAY DIFFRACTIONr_rigid_bond_restr3.29935780
X-RAY DIFFRACTIONr_sphericity_free23.095120
X-RAY DIFFRACTIONr_sphericity_bonded15.65555915
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 204 -
Rwork0.206 3701 -
all-3905 -
obs--93.33 %
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)
10.10510.0282-0.06070.01280.00850.2356-0.0024-0.00470-0.00160.0039-0.00560.001-0.0069-0.00150.0075-0.0018-0.00290.05530.00040.0201138.503315.018628.2516
20.3545-0.0417-0.14230.1278-0.01250.0805-0.0095-0.0312-0.023-0.0124-0.0014-0.0082-0.00120.02370.01090.00710.0028-0.00220.0638-0.00160.0172170.01234.181321.2359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 374
2X-RAY DIFFRACTION2B5 - 373

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