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- PDB-2uyu: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A... -

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Basic information

Entry
Database: PDB / ID: 2uyu
TitleL-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A88F- E192A)
ComponentsRHAMNULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE / AGGREGATION / ZINC ENZYME / FIBRILLATION / METAL-BINDING / OLIGOMERIZATION / INTERFACE DESIGN / SURFACE MUTATION / 2-KETOSE DEGRADATION / PROTEIN-PROTEIN INTERFACE / ZINC / ALDOLASE / CLASS II / RARE SUGAR / CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPH BACTERIAL L-RHAMNOSE METABOLISM / RHAMNOSE METABOLISM / PROTEIN ENGINEERING
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
: / Rhamnulose-1-phosphate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsGrueninger, D. / Schulz, G.E.
Citation
#1: Journal: Biochemistry / Year: 2003
Title: Structure and Catalytic Mechanism of L-Rhamnulose-1-Phosphate Aldolase
Authors: Kroemer, M. / Merkel, I. / Schulz, G.E.
History
DepositionApr 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_asym_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
E: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6276
Polymers60,3852
Non-polymers2434
Water6,143341
1
A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)242,51024
Polymers241,5408
Non-polymers97016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
Buried area34390 Å2
ΔGint-175.2 kcal/mol
Surface area87050 Å2
MethodPQS
2
E: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)242,51024
Polymers241,5408
Non-polymers97016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575y,-x+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation6_577x,-y+2,-z+21
crystal symmetry operation8_777-y+2,-x+2,-z+21
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation5_757-x+2,y,-z+21
Buried area34150 Å2
ΔGint-172.4 kcal/mol
Surface area86540 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.097, 87.097, 170.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-2148-

HOH

21E-2021-

HOH

31E-2148-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 1 - 274 / Label seq-ID: 1 - 274

Dom-IDAuth asym-IDLabel asym-ID
1AA
2EB

NCS oper: (Code: given
Matrix: (-0.7072, -0.707, 0.000623), (-0.707, 0.7072, 0.001686), (-0.001633, 0.000751, -1)
Vector: 148.6, 86.94, 255.5)

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Components

#1: Protein RHAMNULOSE-1-PHOSPHATE ALDOLASE


Mass: 30192.467 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105
References: UniProt: P32169, rhamnulose-1-phosphate aldolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 88 TO PHE ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ALA 88 TO PHE ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ALA ENGINEERED RESIDUE IN CHAIN E, ALA 88 TO PHE ENGINEERED RESIDUE IN CHAIN E, GLU 192 TO ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.1 % / Description: NONE
Crystal growpH: 7.4
Details: 40% (V/V) ETHYLENE GLYCOL, 100 MM HEPES (PH 7.5), 5% (W/V) PEG 3000, RESULTING PH: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.96→20 Å / Num. obs: 47844 / % possible obs: 99.7 % / Observed criterion σ(I): 3.9 / Redundancy: 4.84 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.47
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 4.89 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJR

1ojr


Resolution: 1.96→19.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.479 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3350 7 %RANDOM
Rwork0.201 ---
obs0.204 44494 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2--1.57 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 1.96→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 4 341 4597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224404
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9456010
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.79624.639194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05515710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.7491518
X-RAY DIFFRACTIONr_chiral_restr0.1290.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.22055
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23050
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3540.264
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0481.52842
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55224430
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4831842
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3944.51574
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2126 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.050.05
tight thermal0.230.5
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 242
Rwork0.283 3210

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