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- PDB-2v9e: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E... -

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Basic information

Entry
Database: PDB / ID: 2v9e
TitleL-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A- K248W-A273S)
ComponentsRHAMNULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE / ENTROPY INDEX / METAL-BINDING / OLIGOMERIZATION / ZINC / ALDOLASE / CLASS II / CYTOPLASM / CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONE / BACTERIAL L-RHAMNOSE METABOLISM / INTERFACE DESIGN / SURFACE MUTATION / 2-KETOSE DEGRADATION / PROTEIN-PROTEIN INTERFACE / RARE SUGAR / AGGREGATION / ZINC ENZYME / FIBRILLATION / 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
ACETATE ION / Rhamnulose-1-phosphate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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
DepositionAug 23, 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 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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
B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,06613
Polymers60,3792
Non-polymers68811
Water9,584532
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)122,48732
Polymers120,7584
Non-polymers1,73028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area13370 Å2
ΔGint-64.9 kcal/mol
Surface area46120 Å2
MethodPQS
2
B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,77920
Polymers120,7584
Non-polymers1,02116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-y+3/2,x+3/2,z1
crystal symmetry operation4_365y-3/2,-x+3/2,z1
crystal symmetry operation2_585-x,-y+3,z1
Buried area13650 Å2
ΔGint-69.2 kcal/mol
Surface area46100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)107.520, 107.520, 115.017
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-2017-

HOH

21A-2210-

HOH

31A-2248-

HOH

41B-2110-

HOH

51B-2227-

HOH

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

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: 2 / Auth seq-ID: 1 - 274 / Label seq-ID: 1 - 274

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

NCS oper: (Code: given
Matrix: (-0.1251, 0.9921, 0.0036), (0.9921, 0.1251, -0.01173), (-0.01209, 0.002104, -0.9999)
Vector: -99.66, 93.68, -172.7)

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Components

#1: Protein RHAMNULOSE-1-PHOSPHATE ALDOLASE /


Mass: 30189.400 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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 248 TO TRP ...ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 248 TO TRP ENGINEERED RESIDUE IN CHAIN A, ALA 273 TO SER ENGINEERED RESIDUE IN CHAIN B, GLU 192 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 248 TO TRP ENGINEERED RESIDUE IN CHAIN B, ALA 273 TO SER

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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: 55.4 % / Description: NONE
Crystal growpH: 7.2
Details: 40% (V/V) PEG 400, 0.1M HEPES (PH 7.5), 0.2 M CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.90504
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90504 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 91205 / % possible obs: 98.6 % / Observed criterion σ(I): 5.96 / Redundancy: 8.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.33
Reflection shellHighest resolution: 1.58 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.96 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJR

1ojr


Resolution: 1.58→45.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.383 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 5430 6 %RANDOM
Rwork0.158 ---
obs0.159 85067 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.58→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 26 532 4810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224802
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9426600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.53125.045220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91415777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3021520
X-RAY DIFFRACTIONr_chiral_restr0.1220.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023806
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3160.22529
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.23412
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2429
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.53068
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48124884
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.90631985
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8074.51716
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 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1113tight positional0.110.05
1050medium positional0.630.5
1113tight thermal0.10.5
1050medium thermal0.562
LS refinement shellResolution: 1.58→1.62 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.205 400
Rwork0.17 6277
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)
10.3024-0.2360.09210.6233-0.20580.29710.02560.0239-0.0001-0.0368-0.02040.0556-0.0092-0.0237-0.0052-0.00910.0122-0.0087-0.00850.0052-0.007236.3181126.2113-76.2692
20.1739-0.01160.04880.11040.01480.01670.0064-0.00120.0272-0.0036-0.00960.0053-0.0028-0.00290.0032-0.01070.00310.0002-0.0203-0.0039-0.005748.8373128.7629-54.6483
30.278-0.2933-0.02050.31080.01050.1037-0.0255-0.03750.02390.03690.0429-0.01090.03330.0068-0.01740.01690.0169-0.01720.0105-0.0062-0.017520.7856146.4014-96.6603
40.0807-0.09660.04270.3012-0.07580.27640.00870.04670.0123-0.04230.0052-0.06010.00340.0681-0.01390.0090.00550.01680.0389-0.0054-0.010321.7721158.8928-118.3579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 120
2X-RAY DIFFRACTION2A121 - 274
3X-RAY DIFFRACTION3B1 - 120
4X-RAY DIFFRACTION4B121 - 274

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