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- PDB-4hk5: Crystal structure of Cordyceps militaris IDCase in apo form -

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Basic information

Entry
Database: PDB / ID: 4hk5
TitleCrystal structure of Cordyceps militaris IDCase in apo form
ComponentsUracil-5-carboxylate decarboxylase
KeywordsLYASE / pyrimidine metabolism / DNA decarboxylation / IDCase / decarboxylase / uracil
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 / molecular replacement / Resolution: 1.9 Å
AuthorsXu, S. / 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
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: 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 1.3Sep 20, 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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_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
C: Uracil-5-carboxylate decarboxylase
D: Uracil-5-carboxylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,5979
Polymers168,2704
Non-polymers3275
Water16,772931
1
A: Uracil-5-carboxylate decarboxylase
C: Uracil-5-carboxylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2664
Polymers84,1352
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-131 kcal/mol
Surface area25990 Å2
MethodPISA
2
B: Uracil-5-carboxylate decarboxylase
D: Uracil-5-carboxylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3315
Polymers84,1352
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-151 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.654, 146.163, 77.769
Angle α, β, γ (deg.)90.00, 96.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uracil-5-carboxylate decarboxylase / IDCase


Mass: 42067.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cordyceps militaris (fungus) / Gene: CCM_01452 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: G3J531, EC: 4.1.1.66
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 931 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG3350, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→77.266 Å / Num. obs: 135002 / % possible obs: 99.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.087 / Χ2: 1.022 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.974.60.415134261.0551100
1.97-2.054.60.304135030.9541100
2.05-2.144.60.229134370.9621100
2.14-2.254.60.164134700.9341100
2.25-2.394.60.137135100.9161100
2.39-2.584.60.115135311.0061100
2.58-2.844.60.1134791.1781100
2.84-3.254.60.084135671.3451100
3.25-4.094.50.051135291.028199.9
4.09-504.60.04135500.849199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WM1

2wm1


Resolution: 1.9→77.266 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 6731 5 %RANDOM
Rwork0.1573 ---
obs0.1593 134917 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.3 Å2 / Biso mean: 21.9296 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20.25 Å2
2--0.08 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→77.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11266 0 5 931 12202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911565
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.96715743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88751464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38423.255470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.142151831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.581567
X-RAY DIFFRACTIONr_chiral_restr0.0730.21793
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218752
X-RAY DIFFRACTIONr_rigid_bond_restr1.521311565
X-RAY DIFFRACTIONr_sphericity_free17.3985936
X-RAY DIFFRACTIONr_sphericity_bonded9.254511273
LS refinement shellResolution: 1.9→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 463 -
Rwork0.18 8776 -
all-9239 -
obs-8776 92.11 %

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