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- PDB-2gdq: Crystal structure of mandelate racemase/muconate lactonizing enzy... -

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Basic information

Entry
Database: PDB / ID: 2gdq
TitleCrystal structure of mandelate racemase/muconate lactonizing enzyme from Bacillus subtilis at 1.8 A resolution
ComponentsyitF
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / mandelate racemase/muconate lactonizing enzyme / TIM-barrel / enolase / octamer / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Isomerases / hydro-lyase activity / carbohydrate catabolic process / isomerase activity / magnesium ion binding
Similarity search - Function
: / 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 ...: / 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
Putative isomerase YitF
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Schwinn, K.D. / Emtage, S. / Thompson, D.A. / Rutter, M.E. / Dickey, M. / Groshong, C. / Bain, K.T. ...Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Schwinn, K.D. / Emtage, S. / Thompson, D.A. / Rutter, M.E. / Dickey, M. / Groshong, C. / Bain, K.T. / Adams, J.M. / Reyes, C. / Rooney, I. / Powell, A. / Boice, A. / Gheyi, T. / Ozyurt, S. / Atwell, S. / Wasserman, S.R. / Burley, S.K. / Sali, A. / Babbitt, P. / Pieper, U. / Gerlt, J.A. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of mandelate racemase/muconate lactonizing enzyme from Bacillus subtilis at 1.8 A resolution
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Schwinn, K.D. / Emtage, S. / Thompson, D.A. / Rutter, M.E. / Dickey, M. / Groshong, C. / Bain, K.T. / Adams, J.M. / Reyes, C. / Rooney, I. / ...Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Schwinn, K.D. / Emtage, S. / Thompson, D.A. / Rutter, M.E. / Dickey, M. / Groshong, C. / Bain, K.T. / Adams, J.M. / Reyes, C. / Rooney, I. / Powell, A. / Boice, A. / Gheyi, T. / Ozyurt, S. / Atwell, S. / Wasserman, S.R. / Burley, S.K. / Sali, A. / Babbitt, P. / Pieper, U. / Gerlt, J.A. / Almo, S.C.
History
DepositionMar 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: yitF
B: yitF


Theoretical massNumber of molelcules
Total (without water)86,8032
Polymers86,8032
Non-polymers00
Water13,349741
1
A: yitF
B: yitF

A: yitF
B: yitF

A: yitF
B: yitF

A: yitF
B: yitF


Theoretical massNumber of molelcules
Total (without water)347,2128
Polymers347,2128
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area27170 Å2
ΔGint-101 kcal/mol
Surface area99180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.374, 113.246, 168.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1153-

HOH

21A-1167-

HOH

DetailsThe biological assembly is a octamer generated from the dimer in the asymmetric unit by the operations: -x,1-y,z; x,1-y,-z; -x,y,-z

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Components

#1: Protein yitF


Mass: 43401.492 Da / Num. of mol.: 2 / Fragment: mandelate racemase/muconate lactonizing enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Species: Bacillus subtilis / Strain: 168 / Gene: yitF / Production host: Escherichia coli (E. coli) / References: UniProt: O06741
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium Sulfate, 0.1M Tris, pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 10, 2006 / Details: SGX-CAT
RadiationMonochromator: SGX-CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 72140 / Num. obs: 70561 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.064 / Χ2: 0.969 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2% possible all
1.8-1.8687.440.84562520.62987.4
1.86-1.9494.64.70.63267600.664
1.94-2.0398.34.40.50569921.229
2.03-2.1399.44.80.3171191.021
2.13-2.2799.75.10.17671710.777
2.27-2.4499.64.80.18771191.373
2.44-2.6999.95.70.0972100.902
2.69-3.081006.10.06372100.947
3.08-3.881006.40.0473131.023
3.88-50996.30.02974151.024

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å27.46 Å
Translation2.5 Å27.46 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUC

1muc


Resolution: 1.8→27.46 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.822 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3548 5.1 %RANDOM
Rwork0.197 ---
all0.2 72000 --
obs0.2 70202 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.313 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5958 0 0 741 6699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226123
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9448301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49123.38284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.496151033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6081544
X-RAY DIFFRACTIONr_chiral_restr0.0970.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024694
X-RAY DIFFRACTIONr_nbd_refined0.2080.23084
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24212
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2587
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.256
X-RAY DIFFRACTIONr_mcbond_it1.0291.53832
X-RAY DIFFRACTIONr_mcangle_it1.53325991
X-RAY DIFFRACTIONr_scbond_it2.42632688
X-RAY DIFFRACTIONr_scangle_it3.5944.52310
LS refinement shellResolution: 1.8→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 212 -
Rwork0.327 3965 -
obs-4177 78.52 %

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