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- PDB-2v9f: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E... -

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Basic information

Entry
Database: PDB / ID: 2v9f
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 DIHYDROXYACETONEPH 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 / metal ion binding / identical protein 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: 2.1 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: 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,6228
Polymers30,1891
Non-polymers4327
Water2,288127
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 operation4_545y,-x-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area12600 Å2
ΔGint-72.1 kcal/mol
Surface area44520 Å2
MethodPQS
Unit cell
Length a, b, c (Å)92.832, 92.832, 77.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-2105-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given)

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Components

#1: Protein RHAMNULOSE-1-PHOSPHATE ALDOLASE


Mass: 30189.400 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 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105
References: UniProt: P32169, rhamnulose-1-phosphate aldolase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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
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: 2.8 Å3/Da / Density % sol: 55.3 % / Description: NONE
Crystal growpH: 7.2
Details: 40% (V/V) PEG 400, 0.1 M 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: 0.9
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 17559 / % possible obs: 91.6 % / Observed criterion σ(I): 5 / Redundancy: 7.4 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.68
Reflection shellHighest resolution: 2.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.05 / % possible all: 49.7

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Processing

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

1ojr


Resolution: 2.1→24.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3133262.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1230 7 %RANDOM
Rwork0.185 ---
obs0.185 17559 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.7267 Å2 / ksol: 0.389476 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 19 127 2272
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_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
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: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.216 111 7 %
Rwork0.194 1475 -
obs--49.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMA
X-RAY DIFFRACTION3AC.PARAMAC.TOP
X-RAY DIFFRACTION4WATER.PARAMA
X-RAY DIFFRACTION5WATER_REP.PARAMA

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