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- PDB-4jj9: Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase -

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Basic information

Entry
Database: PDB / ID: 4jj9
TitleCrystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase
Components5-carboxymethyl-2-hydroxymuconate delta-isomerase
KeywordsISOMERASE / NYSGRC / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium / alpha-beeta / trimer / homoprotocatechuate catabolic pathway
Function / homology
Function and homology information


5-carboxymethyl-2-hydroxymuconate Delta-isomerase / 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 delta-isomerase / 5-carboxymethyl-2-hydroxymuconate delta-isomerase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsEswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / 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 5-carboxymethyl-2-hydroxymuconate delta-isomerase
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 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 / struct_site
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 / _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: 5-carboxymethyl-2-hydroxymuconate delta-isomerase
B: 5-carboxymethyl-2-hydroxymuconate delta-isomerase
C: 5-carboxymethyl-2-hydroxymuconate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8187
Polymers55,4343
Non-polymers3844
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-135 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.345, 75.481, 107.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18477.967 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: BB0738, hpaF / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q7WPE6, UniProt: A0A0H3LHY8*PLUS, 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M Ammonium Sulfate, 0.1M Bis Tris, Glycerol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 48870 / Num. obs: 48870 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 18.1
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.308 / Num. unique all: 3805 / % possible all: 94.5

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.248 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23438 2467 5.1 %RANDOM
Rwork0.2118 ---
all0.227 48693 --
obs0.21293 46226 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.069 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 20 116 3557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213497
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.9674723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9045445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52222.584178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28815546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4181542
X-RAY DIFFRACTIONr_chiral_restr0.0710.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212750
X-RAY DIFFRACTIONr_mcbond_it0.5681.52196
X-RAY DIFFRACTIONr_mcangle_it1.12523448
X-RAY DIFFRACTIONr_scbond_it2.04431301
X-RAY DIFFRACTIONr_scangle_it3.1294.51275
LS refinement shellResolution: 1.764→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 172 -
Rwork0.247 3202 -
obs-3374 94.56 %

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