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Basic information

Entry
Database: PDB / ID: 3bjs
TitleCrystal structure of a member of enolase superfamily from Polaromonas sp. JS666
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ENOLASE / RACEMASE / PSI-2 / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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 ...Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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
Mandelate racemase/muconate lactonizing enzyme
Similarity search - Component
Biological speciesPolaromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsPatskovsky, Y. / Bonanno, J.B. / Ozyurt, S. / Dickey, M. / Sauder, J.M. / Reyes, C. / Groshong, C. / Gheyi, T. / Smith, D. / Wasserman, S.R. ...Patskovsky, Y. / Bonanno, J.B. / Ozyurt, S. / Dickey, M. / Sauder, J.M. / Reyes, C. / Groshong, C. / Gheyi, T. / Smith, D. / Wasserman, S.R. / Gerlt, J. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a Member of Enolase Superfamily from Polaromonas sp. JS666.
Authors: Patskovsky, Y. / Bonanno, J.B. / Ozyurt, S. / Dickey, M. / Sauder, J.M. / Reyes, C. / Groshong, C. / Gheyi, T. / Smith, D. / Wasserman, S.R. / Gerlt, J. / Burley, S.K. / Almo, S.C.
History
DepositionDec 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4834
Polymers93,4352
Non-polymers492
Water48627
1
A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,93316
Polymers373,7388
Non-polymers1948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_524x,-y-3,-z-11
crystal symmetry operation20_536x,-z-2,y+11
crystal symmetry operation17_543x,z-1,-y-21
Buried area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.640, 274.640, 274.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 37 - 410 / Label seq-ID: 39 - 412

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Mandelate racemase/muconate lactonizing enzyme


Mass: 46717.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. (bacteria) / Strain: JS666 / Gene: Bpro_5118 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q120Q7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 2000 MME, 150mM Potassium bromide pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 21, 2007
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24915 / % possible obs: 99.2 % / Observed criterion σ(I): -0.5 / Redundancy: 7.8 % / Biso Wilson estimate: 57.55 Å2 / Rmerge(I) obs: 0.18 / Rsym value: 0.173 / Net I/σ(I): 3.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.207 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 1.3 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26337 795 3.2 %RANDOM
Rwork0.20519 ---
obs0.20701 23986 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.227 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5641 0 2 27 5670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225827
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9597908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8815756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11322.915247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97315948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4041549
X-RAY DIFFRACTIONr_chiral_restr0.0820.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024447
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1250.32755
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.53914
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.5302
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.384
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8571.53814
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.66625937
X-RAY DIFFRACTIONr_scbond_it8.66432278
X-RAY DIFFRACTIONr_scangle_it11.7794.51963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2809 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.250.5
2Bmedium thermal3.11.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 61 -
Rwork0.336 1684 -
obs--98.09 %

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