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- PDB-2v9g: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT Q... -

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Basic information

Entry
Database: PDB / ID: 2v9g
TitleL-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT Q6Y- L84W-E192A)
ComponentsRHAMNULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE / ZINC / ALDOLASE / CLASS II / CYTOPLASM / PROTEIN ENGINEERING / 2-KETOSE DEGRADATION / CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPH BACTERIAL L-RHAMNOSE METABOLISM / METAL-BINDING / OLIGOMERIZATION / INTERFACE DESIGN / PROTEIN-PROTEIN INTERFACE / RARE SUGAR / AGGREGATION / ZINC ENZYME / FIBRILLATION / SURFACE MUTATION / RHAMNOSE METABOLISM
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
L(+)-TARTARIC ACID / Rhamnulose-1-phosphate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 22, 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
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_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_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_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
B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
C: RHAMNULOSE-1-PHOSPHATE ALDOLASE
D: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,91013
Polymers120,8984
Non-polymers1,0129
Water2,234124
1
A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
C: RHAMNULOSE-1-PHOSPHATE ALDOLASE
D: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: RHAMNULOSE-1-PHOSPHATE ALDOLASE
B: RHAMNULOSE-1-PHOSPHATE ALDOLASE
C: RHAMNULOSE-1-PHOSPHATE ALDOLASE
D: RHAMNULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,82026
Polymers241,7968
Non-polymers2,02418
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area26260 Å2
ΔGint-143.7 kcal/mol
Surface area87140 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.902, 100.825, 270.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given)

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Components

#1: Protein
RHAMNULOSE-1-PHOSPHATE ALDOLASE /


Mass: 30224.467 Da / Num. of mol.: 4 / 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-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 6 TO TYR ENGINEERED RESIDUE IN CHAIN A, LEU 84 TO TRP ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, GLN 6 TO TYR ENGINEERED RESIDUE IN CHAIN A, LEU 84 TO TRP ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 6 TO TYR ENGINEERED RESIDUE IN CHAIN B, LEU 84 TO TRP ENGINEERED RESIDUE IN CHAIN B, GLU 192 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLN 6 TO TYR ENGINEERED RESIDUE IN CHAIN C, LEU 84 TO TRP ENGINEERED RESIDUE IN CHAIN C, GLU 192 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLN 6 TO TYR ENGINEERED RESIDUE IN CHAIN D, LEU 84 TO TRP ENGINEERED RESIDUE IN CHAIN D, GLU 192 TO ALA
Sequence detailsRHAD_ECOLI

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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: 2.5 Å3/Da / Density % sol: 50.5 % / Description: NONE
Crystal growpH: 7.7 / Details: 1 M NA/K-TARTRATE, 0.1 M HEPES (PH 7.7)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 2.67→15 Å / Num. obs: 32949 / % possible obs: 95.2 % / Observed criterion σ(I): 3.4 / Redundancy: 3.63 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.77
Reflection shellHighest resolution: 2.67 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.4 / % possible all: 85.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GT7

1gt7


Resolution: 2.7→14.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 6403000.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2243 7 %RANDOM
Rwork0.218 ---
obs0.218 32036 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.9476 Å2 / ksol: 0.354928 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-15.06 Å20 Å20 Å2
2---3.87 Å20 Å2
3----11.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8508 0 54 124 8686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 338 7 %
Rwork0.284 4499 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3DTAR.PARAMDTAR.TOP
X-RAY DIFFRACTION4WATER.PARAM
X-RAY DIFFRACTION5WATER_REP.PARAM

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