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- PDB-3u9i: The crystal structure of Mandelate racemase/muconate lactonizing ... -

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Basic information

Entry
Database: PDB / ID: 3u9i
TitleThe crystal structure of Mandelate racemase/muconate lactonizing enzyme from Roseiflexus sp.
ComponentsMandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
KeywordsISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / metal ion binding
Similarity search - Function
Dipeptide epimerase / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...Dipeptide epimerase / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRoseiflexus sp. RS-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of Mandelate racemase/muconate lactonizing enzyme from Roseiflexus sp.
Authors: Zhang, Z. / Almo, S.C. / Swaminathan, S.
History
DepositionOct 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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_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

Downloads & links

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Assembly

Deposited unit
A: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
B: Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7574
Polymers82,5642
Non-polymers1922
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-42 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.888, 209.888, 116.601
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Mandelate racemase/muconate lactonizing enzyme, C-terminal domain protein


Mass: 41282.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseiflexus sp. RS-1 (bacteria) / Gene: RoseRS_2982 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5UXJ3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M bis-tris pH 5.5, 2.0 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 21881 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 15.04
Reflection shellResolution: 2.9→3 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2173 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3IK4

3ik4


Resolution: 2.9→49.072 Å / SU ML: 0.42 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.21 / Phase error: 25.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 1043 4.97 %RANDOM
Rwork0.1994 ---
obs0.2022 20973 95.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.216 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.0962 Å2-0 Å2-0 Å2
2--8.0962 Å20 Å2
3----16.1924 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5123 0 10 67 5200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055214
X-RAY DIFFRACTIONf_angle_d0.9357102
X-RAY DIFFRACTIONf_dihedral_angle_d17.7611854
X-RAY DIFFRACTIONf_chiral_restr0.057878
X-RAY DIFFRACTIONf_plane_restr0.004917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.0530.30511420.24692648X-RAY DIFFRACTION90
3.053-3.24420.29831330.23692758X-RAY DIFFRACTION93
3.2442-3.49460.30051600.22792776X-RAY DIFFRACTION95
3.4946-3.84620.2571430.20662822X-RAY DIFFRACTION95
3.8462-4.40240.21871660.16662919X-RAY DIFFRACTION99
4.4024-5.54540.22011540.16112965X-RAY DIFFRACTION99
5.5454-49.07880.25491450.1993042X-RAY DIFFRACTION99

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