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- PDB-2v29: L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT K15W) -

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Basic information

Entry
Database: PDB / ID: 2v29
TitleL-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT K15W)
ComponentsRHAMNULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE / ZINC ENZYME / METAL-BINDING / SURFACE MUTATION / 2-KETOSE DEGRADATION / PROTEIN-PROTEIN INTERFACE / ALDOLASE / CLASS II / RARE SUGAR / CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONE PHOSPHATE / BACTERIAL L-RHAMNOSE METABOLISM / RHAMNOSE METABOLISM / PROTEIN ENGINEERING / DOMAIN MOTION FOR MECHANICAL SUPPORT OF CATALYSIS
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: 2 Å
AuthorsGrueninger, D. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 2008
Title: Antenna Domain Mobility and Enzymatic Reaction of L-Rhamnulose-1-Phosphate Aldolase.
Authors: Grueninger, D. / Schulz, G.E.
#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
DepositionJun 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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_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.ptnr1_symmetry / _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 / _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_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_conn.ptnr2_symmetry

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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)61,39917
Polymers60,4632
Non-polymers93615
Water6,575365
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)123,45144
Polymers120,9264
Non-polymers2,52540
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,-x+1,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area13530 Å2
ΔGint-80.2 kcal/mol
Surface area46600 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)122,14324
Polymers120,9264
Non-polymers1,21720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_365y-2,-x+1,z1
crystal symmetry operation3_675-y+1,x+2,z1
crystal symmetry operation2_485-x-1,-y+3,z1
Buried area13320 Å2
ΔGint-78.4 kcal/mol
Surface area46170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)82.873, 82.873, 98.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein RHAMNULOSE-1-PHOSPHATE ALDOLASE /


Mass: 30231.436 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.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 15 TO TRP ENGINEERED RESIDUE IN CHAIN B, LYS 15 TO TRP

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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: 56.1 % / Description: NONE
Crystal growpH: 4.5
Details: 100 MM SODIUM ACETATE PH 4.5, 50% (V/V) ETHYLENEGLYCOL, 5% (V/V) PEG 1000

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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: 2→50 Å / Num. obs: 44803 / % possible obs: 100 % / Observed criterion σ(I): 4.17 / Redundancy: 4.26 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.29
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 4.17 / % possible all: 100

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Processing

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

1ojr


Resolution: 2→42.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.181 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3137 7 %RANDOM
Rwork0.161 ---
obs0.164 41666 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 45 365 4668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224400
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9475984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.55124.526190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65615694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3181518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023350
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22142
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23026
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2314
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0730.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8271.52812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31624394
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1331856
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1544.51590
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: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 230 -
Rwork0.17 3053 -
obs--100 %
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)
10.6427-0.50281.01221.4872-1.05371.76360.0853-0.036-0.0455-0.19920.00170.27490.1676-0.0005-0.087-0.01750.0327-0.038-0.05920.01310.0138-23.587391.7721-110.9158
20.9452-0.06710.20910.41520.09880.31040.0176-0.07920.14190.08970.00140.0998-0.0871-0.0391-0.0190.0070.02750.0452-0.0235-0.03-0.0136-14.264999.6502-89.2343
31.09410.156-0.45551.39590.93631.52020.00350.1892-0.13-0.07240.1379-0.2559-0.03230.1211-0.1414-0.02730.02530.01720.0268-0.0954-0.0292-22.5468107.6941-156.2227
40.6785-0.066-0.08180.4385-0.04930.40680.0748-0.0178-0.13940.03940.0156-0.03930.11220.0231-0.09040.0160.0195-0.0472-0.0392-0.0071-0.0104-33.9433103.5829-134.4665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 117
2X-RAY DIFFRACTION2A118 - 273
3X-RAY DIFFRACTION3B2 - 117
4X-RAY DIFFRACTION4B118 - 273

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