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- PDB-4pfz: X-ray Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delt... -

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Basic information

Entry
Database: PDB / ID: 4pfz
TitleX-ray Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase from Mycobacterium smegmatis
Components5-carboxymethyl-2-hydroxymuconate delta-isomerase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


Rv2993c-like, N-terminal / Rv2993c-like, N-terminal / FAH / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / SH3 type barrels. / Roll ...Rv2993c-like, N-terminal / Rv2993c-like, N-terminal / FAH / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5-carboxymethyl-2-hydroxymuconate delta-isomerase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHoranyi, P.S. / Abendroth, J. / Lorimer, D. / Edwards, T. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: X-ray Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase from Mycobacterium smegmatis
Authors: Horanyi, P.S. / Abendroth, J. / Lorimer, D. / Edwards, T.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-carboxymethyl-2-hydroxymuconate delta-isomerase
B: 5-carboxymethyl-2-hydroxymuconate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4074
Polymers55,3612
Non-polymers462
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-34 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.000, 53.740, 69.750
Angle α, β, γ (deg.)90.00, 107.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

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Components

#1: Protein 5-carboxymethyl-2-hydroxymuconate delta-isomerase / / Putative 2-hydroxyhepta-2 / 4-diene-1 / 7-dioate isomerase


Mass: 27680.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2382, MSMEI_2322 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0QUY6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 1500, 100mM SPG pH 6.0 SPG: succinic acid, NaH2PO4 H20, glycine, pH adjusted with 10M NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2010
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 44763 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.45 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.73
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.2 / % possible all: 97.2

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rr6

3rr6


Resolution: 1.8→40.74 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2000 4.47 %Random
Rwork0.195 ---
obs0.196 46762 --
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.88 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 2 331 4026
Refinement TLS params.Method: refined / Origin x: 11.7025 Å / Origin y: -4.8384 Å / Origin z: 15.3459 Å
111213212223313233
T0.1358 Å2-0.0237 Å2-0.0264 Å2-0.1176 Å20.0091 Å2--0.1123 Å2
L2.2885 °2-0.7835 °2-0.6914 °2-1.7626 °20.4247 °2--1.3151 °2
S0.0218 Å °-0.113 Å °-0.1161 Å °0.0186 Å °-0.0171 Å °-0.1042 Å °0.0573 Å °0.0691 Å °-0.0042 Å °

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