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

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Basic information

Entry
Database: PDB / ID: 3ssz
TitleThe crystal structure of Mandelate racemase/muconate lactonizing enzyme from Rhodobacteraceae bacterium
ComponentsMandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
KeywordsMETAL BINDING PROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / enolase
Function / homology
Function and homology information


L-rhamnonate dehydratase / L-rhamnonate dehydratase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
L-lyxonate dehydratase / L-rhamnonate dehydratase / : / 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 ...L-lyxonate dehydratase / L-rhamnonate dehydratase / : / 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
L-rhamnonate dehydratase
Similarity search - Component
Biological speciesRhodobacteraceae bacterium KLH11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.392 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 Rhodobacteraceae bacterium
Authors: Zhang, Z. / Almo, S.C. / Swaminathan, S.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,6952
Polymers46,5991
Non-polymers961
Water1,874104
1
A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)373,55916
Polymers372,7918
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area41540 Å2
ΔGint-252 kcal/mol
Surface area84480 Å2
MethodPISA
2
A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3904
Polymers93,1982
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4390 Å2
ΔGint-45 kcal/mol
Surface area27120 Å2
MethodPISA
3
A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3904
Polymers93,1982
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area3130 Å2
ΔGint-40 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.777, 136.777, 116.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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


Mass: 46598.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacteraceae bacterium KLH11 (bacteria)
Gene: RKLH11_3829 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B9NY46
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 2.0 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: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 22070 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 24.5
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 17.5 / Num. unique all: 2163 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FXG

3fxg


Resolution: 2.392→48.358 Å / SU ML: 0.63 / Isotropic thermal model: Isotropic / σ(F): 1.4 / Phase error: 21.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1130 5.12 %RANDOM
Rwork0.1835 ---
obs0.186 22063 99.9 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.321 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1321 Å20 Å20 Å2
2---0.1321 Å20 Å2
3---0.2641 Å2
Refinement stepCycle: LAST / Resolution: 2.392→48.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 5 104 3127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083107
X-RAY DIFFRACTIONf_angle_d1.14217
X-RAY DIFFRACTIONf_dihedral_angle_d15.1061133
X-RAY DIFFRACTIONf_chiral_restr0.07449
X-RAY DIFFRACTIONf_plane_restr0.005541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3917-2.50050.29561370.20722551X-RAY DIFFRACTION99
2.5005-2.63230.27981550.20442559X-RAY DIFFRACTION100
2.6323-2.79730.26661300.20962590X-RAY DIFFRACTION100
2.7973-3.01320.28811370.20822586X-RAY DIFFRACTION100
3.0132-3.31640.26891560.21142597X-RAY DIFFRACTION100
3.3164-3.79610.25141600.19262597X-RAY DIFFRACTION100
3.7961-4.7820.18561340.14872654X-RAY DIFFRACTION100
4.782-48.36780.18551210.1692799X-RAY DIFFRACTION100

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