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- PDB-1dzx: L-Fuculose-1-Phosphate Aldolase from Escherichia coli Mutant R212A -

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Basic information

Entry
Database: PDB / ID: 1dzx
TitleL-Fuculose-1-Phosphate Aldolase from Escherichia coli Mutant R212A
ComponentsL-fuculose phosphate aldolase
KeywordsLYASE (ALDEHYDE) / ALDOLASE (CLASS II) / BACTERIAL L-FUCOSE METABOLISM / CLEAVAGE OF L-FUCULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPHOSPHATE AND L-LACTALDEHYDE / MUTANT STRUCTURE
Function / homology
Function and homology information


arabinose catabolic process / L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / D-arabinose catabolic process / L-fucose catabolic process / pentose catabolic process / aldehyde-lyase activity / zinc ion binding / cytosol
Similarity search - Function
L-fucose phosphate aldolase / : / L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / L-fuculose phosphate aldolase / L-fuculose phosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.18 Å
AuthorsJoerger, A.C. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 2000
Title: Catalytic Action of Fuculose 1-Phosphate Aldolase (Class II) as Derived from Structure-Directed Mutagenesis
Authors: Joerger, A.C. / Gosse, C. / Fessner, W.-D. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Catalytic Mechanism of the Metal-Dependent Fuculose Aldolase from Escherichia Coli as Derived from the Structure
Authors: Dreyer, M.K. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: The Spatial Structure of the Class II L-Fuculose-1-Phosphate Aldolase from Escherichia Coli
Authors: Dreyer, M.K. / Schulz, G.E.
History
DepositionMar 7, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: diffrn_source / exptl_crystal_grow ...diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _diffrn_source.pdbx_synchrotron_y_n / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_status / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: L-fuculose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0555
Polymers23,7191
Non-polymers3364
Water1,76598
1
P: L-fuculose phosphate aldolase
hetero molecules

P: L-fuculose phosphate aldolase
hetero molecules

P: L-fuculose phosphate aldolase
hetero molecules

P: L-fuculose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,21920
Polymers94,8774
Non-polymers1,34316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.700, 93.700, 42.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein L-fuculose phosphate aldolase / D-ribulose-phosphate aldolase / L-fuculose-1-phosphate aldolase


Mass: 23719.203 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: R212A SUBSTITUTION PERFORMED WITH KUNKEL METHOD USING M13MP19
Gene: fucA, fucA_1, fucA_2, A9R57_06860, ACU57_24310, AM464_05705, AUQ13_17640, BANRA_01321, BANRA_04164, BANRA_04304, BHS87_15835, BJJ90_05160, BUE81_06870, BvCms12BK_05168, BvCms2454_02072, ...Gene: fucA, fucA_1, fucA_2, A9R57_06860, ACU57_24310, AM464_05705, AUQ13_17640, BANRA_01321, BANRA_04164, BANRA_04304, BHS87_15835, BJJ90_05160, BUE81_06870, BvCms12BK_05168, BvCms2454_02072, BvCmsHHP001_01136, BvCmsHHP056_02000, BvCmsKKP061_04411, BvCmsKSP011_02414, BvCmsKSP024_03378, BvCmsKSP026_00082, BvCmsKSP040_03336, BvCmsKSP045_02228, BvCmsKSP067_03660, BvCmsNSNP027_02922, BvCmsNSP047_01577, BvCmsSINP012_00041, BW690_04870, C4J69_11555, C9E25_03225, CV83915_03318, D2185_02685, D3821_11040, D3Y67_10455, D9D20_04550, D9E35_20280, D9H68_17240, DP258_16175, E5M00_06120, EAI52_12600, EC3234A_48c01090, ECTO6_01047, EEP23_13950, EFB45_09210, EL75_0893, EL79_0895, EL80_0898, EPS71_16910, EPT01_16955, ERS085365_02448, ERS085366_03061, ERS085416_02919, ERS139211_02051, ERS150873_02024, EXX32_11695, EXX39_16005, EXX71_16135, HmCms184_04796, NCTC11181_03256, NCTC13462_04786, NCTC8500_01060, NCTC9037_01222, NCTC9045_01197, NCTC9058_00868, NCTC9062_02153, NCTC9706_03275, RK56_023265, SAMEA3472047_00318, SAMEA3472080_03134, SAMEA3484427_03277, SAMEA3484429_03394, SAMEA3752559_02974, SAMEA3753300_01128, SK85_03044, WR15_06195
Plasmid: PKKFA2-R212A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM 105
References: UniProt: A0A037YR34, UniProt: P0AB87*PLUS, L-fuculose-phosphate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN P ENGINEERED MUTATION ARG212ALA
Sequence detailsTHR: THE 7 C-TERMINAL RESIDUES (TYR 209 - GLU 215) WERE NOT SEEN IN THE DENSITY MAPS

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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 Å3/Da / Density % sol: 38 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: CRYSTALS GROWN FROM AMMONIUM SULFATE AT PH 8.0,VAPOUR DIFFUSION, HANGING DROP,CONDITIONS CLOSE TO THE ONES REPORTED FOR THE WILD-TYPE, SEE PDB ID 1FUA FOR FURTHER DETAILS

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS XP-18H / Wavelength: 1.5418
DetectorType: SIEMENS X-1000 CCD / Detector: CCD / Date: Apr 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→10 Å / Num. obs: 9269 / % possible obs: 89 % / Redundancy: 3.9 % / Rsym value: 0.034
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 1.9 % / Rsym value: 0.17 / % possible all: 65

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 2.18→10 Å / SU B: 3.3 / SU ML: 0.08 / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2 -6 %RANDOM
Rwork0.146 ---
obs-9269 89 %-
Displacement parametersBiso mean: 25.5 Å2
Refinement stepCycle: LAST / Resolution: 2.18→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 15 98 1722
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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