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- PDB-4jcu: Crystal structure of a 5-carboxymethyl-2-hydroxymuconate isomeras... -

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Basic information

Entry
Database: PDB / ID: 4jcu
TitleCrystal structure of a 5-carboxymethyl-2-hydroxymuconate isomerase from Deinococcus radiodurans R1
Components5-carboxymethyl-2-hydroxymuconate isomerase
KeywordsISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / alpha/beta / Triangular trimer assembly / PROTEIN STRUCTURE INITIATIVE / 5-carboxymethyl-2-hydroxymuconate
Function / homology
Function and homology information


5-carboxymethyl-2-hydroxymuconate delta-isomerase activity / catabolic process
Similarity search - Function
5-carboxymethyl-2-hydroxymuconate isomerase / 5-carboxymethyl-2-hydroxymuconate isomerase / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-carboxymethyl-2-hydroxymuconate isomerase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a 5-carboxymethyl-2-hydroxymuconate isomerase from Deinococcus radiodurans R1
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-carboxymethyl-2-hydroxymuconate isomerase
B: 5-carboxymethyl-2-hydroxymuconate isomerase
C: 5-carboxymethyl-2-hydroxymuconate isomerase


Theoretical massNumber of molelcules
Total (without water)51,2153
Polymers51,2153
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-29 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.341, 157.341, 38.197
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein 5-carboxymethyl-2-hydroxymuconate isomerase


Mass: 17071.732 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_A0227 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RYT1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate, 25% PEG 4000, 5% Trimethylamine N-oxide dihydrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2013 / Details: Mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 21677 / Num. obs: 21677 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.8
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2 / Num. unique all: 1749 / % possible all: 99

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→45.46 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.082 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.319 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26215 1110 5.1 %RANDOM
Rwork0.20377 ---
obs0.20669 20556 99.82 %-
all-20556 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.276 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å2-1.75 Å20 Å2
2---1.75 Å20 Å2
3---5.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 0 39 3196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193228
X-RAY DIFFRACTIONr_bond_other_d0.0020.023075
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9754368
X-RAY DIFFRACTIONr_angle_other_deg0.89337065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5545395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35223.333159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96215524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5721528
X-RAY DIFFRACTIONr_chiral_restr0.0980.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02765
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 83 -
Rwork0.284 1487 -
obs--98.87 %

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