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- PDB-3kao: Crystal structure of tagatose 1,6-diphosphate aldolase from Staph... -

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Basic information

Entry
Database: PDB / ID: 3kao
TitleCrystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus
ComponentsTagatose 1,6-diphosphate aldolase
KeywordsLYASE / tagatose 1 / 6-diphosphate aldolase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Lactose metabolism
Function / homology
Function and homology information


tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / 6-deoxy-6-sulfofructose-1-phosphate aldolase activity / lactose catabolic process via tagatose-6-phosphate / 6-sulfoquinovose(1-) catabolic process / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity
Similarity search - Function
Tagatose 1,6-diphosphate aldolase / : / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Tagatose 1,6-diphosphate aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsChang, C. / Marshall, N. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus
Authors: Chang, C. / Marshall, N. / Cobb, G. / Joachimiak, A.
History
DepositionOct 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Tagatose 1,6-diphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,90710
Polymers37,1461
Non-polymers7619
Water7,242402
1
A: Tagatose 1,6-diphosphate aldolase
hetero molecules

A: Tagatose 1,6-diphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,81420
Polymers74,2922
Non-polymers1,52118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5490 Å2
ΔGint-280 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.704, 84.704, 202.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

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Components

#1: Protein Tagatose 1,6-diphosphate aldolase / Tagatose-bisphosphate aldolase / D-tagatose-1 / 6-bisphosphate aldolase


Mass: 37146.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699
Gene: lacD, SAV2192, Staphylococcus aureus subsp. aureus Mu50
Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)magic / References: UniProt: P0A009, tagatose-bisphosphate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.9 Å3/Da / Density % sol: 74.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mM zinc sulfate, 100 mM MES pH 6.5, 12.5 % PEG550 MME, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2009
RadiationMonochromator: Si(111)double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 59080 / Num. obs: 59016 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 54.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 6.43 / Num. unique all: 2889 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.355 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17098 2984 5.1 %RANDOM
Rwork0.14821 ---
all0.14935 58917 --
obs0.14935 58917 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 36 402 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222861
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.973895
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5325368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36825.532141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46715509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9591514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212223
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.591.51753
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09722841
X-RAY DIFFRACTIONr_scbond_it2.14531108
X-RAY DIFFRACTIONr_scangle_it3.5954.51054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 205 -
Rwork0.193 4057 -
obs-4262 99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.66290.29410.27511.45340.4810.67390.00830.0938-0.0235-0.1914-0.01050.0256-0.00360.04410.00220.12620.0064-0.03450.0165-0.0020.018923.856628.080277.9065
21.1644-0.18110.17271.0557-0.36061.0813-0.0228-0.0514-0.0261-0.06010.09250.18070.0212-0.1864-0.06970.0287-0.0045-0.02810.04080.02150.046915.62731.11595.4539
30.8166-0.15490.02351.360.06770.7225-0.00760.06340.0598-0.25880.04770.2108-0.1339-0.1201-0.04010.13540.0049-0.08490.04250.03670.091712.314340.432377.1259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 90
2X-RAY DIFFRACTION2A91 - 200
3X-RAY DIFFRACTION3A201 - 326

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