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- PDB-1ojr: L-rhamnulose-1-phosphate aldolase from Escherichia coli (mutant E192A) -

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Basic information

Entry
Database: PDB / ID: 1ojr
TitleL-rhamnulose-1-phosphate aldolase from Escherichia coli (mutant E192A)
ComponentsRHAMNULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE / ALDOLASE (LYASE) / CLASS II / ZINC ENZYME / C4-TETRAMER / BACTERIAL L-RHAMNOSE METABOLISM / CLEAVAGE OF L-RHAMNULOSE-1- PHOSPHATE TO DIHYDROXYACETONEPHOSPHATE AND L-LACTALDEHYDE
Function / homology
Function and homology information


rhamnulose-1-phosphate aldolase / rhamnulose-1-phosphate aldolase activity / rhamnose catabolic process / pentose catabolic process / aldehyde-lyase activity / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Rhamnulose-1-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
Dihydroxyacetone / 1,4-DIETHYLENE DIOXIDE / PHOSPHATE ION / Rhamnulose-1-phosphate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKroemer, M. / Merkel, I. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 2003
Title: Structure and Catalytic Mechanism of L-Rhamnulose-1-Phosphate Aldolase.
Authors: Kroemer, M. / Merkel, I. / Schulz, G.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The Structure of L-Rhamnulose-1-Phosphate Aldolase (Class II) Solved by Low-Resolution Sir Phasing and 20-Fold Ncs Averaging
Authors: Kroemer, M. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: Structures of L-Fuculose-1-Phosphate Aldolase Mutants Outlining Motions During Catalysis
Authors: Joerger, A.C. / Mueller-Dieckmann, C. / Schulz, G.E.
#3: Journal: J.Bacteriol. / Year: 1993
Title: Sequencing and Characterization of a Gene Cluster Encoding the Enzymes for L-Rhamnose Metabolism in Escherichia Coli
Authors: Moralejo, P. / Egan, S.M. / Hidalgo, E. / Aguilar, J.
History
DepositionJul 15, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,91810
Polymers30,1161
Non-polymers8029
Water9,458525
1
A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,67340
Polymers120,4654
Non-polymers3,20836
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)108.024, 108.024, 57.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-2113-

HOH

21A-2253-

HOH

31A-2439-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein RHAMNULOSE-1-PHOSPHATE ALDOLASE


Mass: 30116.369 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKK223-3 (GEN RHAD) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105
References: UniProt: P32169, rhamnulose-1-phosphate aldolase
#4: Sugar ChemComp-2HA / Dihydroxyacetone


Type: saccharide / Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3

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Non-polymers , 5 types, 533 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUES GLU 192 ALA (SURFACE MUTATION)

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4
Details: HANGING DROP WITH 5 MG/ML PROTEIN AND 18% (V/V) DIOXANE. RESERVOIR WITH 35% (V/V) DIOXANE. HAMPTON CRYSTAL SCREEN-2 NO.4, pH 4.00
Crystal grow
*PLUS
pH: 3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMpotassium phosphate1reservoirpH3.0
235 %(v/v)dioxane1reservoir
310 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8468
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8468 Å / Relative weight: 1
ReflectionResolution: 1.35→30.5 Å / Num. obs: 71387 / % possible obs: 96 % / Redundancy: 3.7 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 8.7
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.7 / % possible all: 95
Reflection
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 30.5 Å / % possible obs: 96 % / Redundancy: 3.7 %
Reflection shell
*PLUS
% possible obs: 95 % / Redundancy: 3.4 % / Num. unique obs: 7660 / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GT7

1gt7


Resolution: 1.35→30.43 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.647 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO ADDITIONAL DENSITY REGIONS IN THE ACTIVE CENTER WERE FITTED BY A 1:1 MIXTURE OF DIHYDROXYACETONE AND PHOSPHATE AND A 1:1 MIXTURE OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO ADDITIONAL DENSITY REGIONS IN THE ACTIVE CENTER WERE FITTED BY A 1:1 MIXTURE OF DIHYDROXYACETONE AND PHOSPHATE AND A 1:1 MIXTURE OF PHOSPHATE AND FIVE WATER MOLECULES, RESPECTIVELY. DIHYDROXYACETONE WAS AN 0.2% (V/V) IMPURITY IN THE AUTOCLAVED CRYO PROTECTANT GLYCEROL. THE PHOSPHATE WAS FROM THE LAST PURIFICATION BUFFER AND HAD ESCAPED DIALYSIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.142 2175 3 %RANDOM
Rwork0.111 ---
obs0.112 69212 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2120 0 47 525 2692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222338
X-RAY DIFFRACTIONr_bond_other_d0.0010.022134
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9583208
X-RAY DIFFRACTIONr_angle_other_deg1.11235028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0673294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77615435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022544
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02441
X-RAY DIFFRACTIONr_nbd_refined0.2290.3553
X-RAY DIFFRACTIONr_nbd_other0.1880.32103
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.2290.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.5425
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1790.52
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.53
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.360
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.567
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.84221407
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.69642322
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8964931
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.996877
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 148
Rwork0.209 4849
Refinement
*PLUS
Lowest resolution: 30.5 Å / % reflection Rfree: 3.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.25

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