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- PDB-2vws: Crystal structure of YfaU, a metal ion dependent class II aldolas... -

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Basic information

Entry
Database: PDB / ID: 2vws
TitleCrystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12
ComponentsYFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
KeywordsLYASE / ESCHERICHIA COLI K-12 PROTEIN YFAU / 2-KETO-3-DEOXY SUGAR ALDOLASE / DEGRADATION OF HOMOPROTOCATECHUATE / CLASS II ALDOLASE / (BETA/ALPHA)8 BARREL
Function / homology
Function and homology information


2-keto-3-deoxy-L-rhamnonate aldolase / 2-keto-3-deoxy-L-rhamnonate aldolase activity / 2-dehydro-3-deoxy-D-gluconate aldolase activity / aldehyde-lyase activity / protein hexamerization / nickel cation binding / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
2-keto-3-deoxy-L-rhamnonate aldolase / : / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 2-keto-3-deoxy-L-rhamnonate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsRea, D. / Rakus, J.F. / Gerlt, J.A. / Fulop, V. / Bugg, T.D.H. / Roper, D.I.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal Structure and Functional Assignment of Yfau, a Metal Ion Dependent Class II Aldolase from Escherichia Coli K12.
Authors: Rea, D. / Hovington, R. / Rakus, J.F. / Gerlt, J.A. / Fulop, V. / Bugg, T.D.H. / Roper, D.I.
History
DepositionJun 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
B: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
C: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3939
Polymers86,8293
Non-polymers5646
Water17,276959
1
A: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
B: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
C: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
hetero molecules

A: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
B: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
C: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,78618
Polymers173,6586
Non-polymers1,12812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area28320 Å2
ΔGint-211.1 kcal/mol
Surface area62050 Å2
MethodPQS
Unit cell
Length a, b, c (Å)105.200, 136.800, 123.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2078-

HOH

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Components

#1: Protein YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE / UNCHARACTERIZED PROTEIN YFAU


Mass: 28942.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PT7-7-YFAU / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P76469, 2-dehydro-3-deoxyglucarate aldolase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / Source method: isolated from a natural source / Formula: H2O

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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: 47 % / Description: NONE
Crystal growpH: 6.5
Details: WRIGHT, A., BLEWETT, A., FULOP, V., COOPER, R., BURROWS, S., JONES, C. & ROPER, D. (2002). EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY CHARACTERIZATION OF AN HHED ALDOLASE ...Details: WRIGHT, A., BLEWETT, A., FULOP, V., COOPER, R., BURROWS, S., JONES, C. & ROPER, D. (2002). EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY CHARACTERIZATION OF AN HHED ALDOLASE HOMOLOGUE FROM ESCHERICHIA COLI K12. ACTA CRYST. D58, 2191-2193., pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 20, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.39→60 Å / Num. obs: 176395 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.2
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DXE

1dxe


Resolution: 1.39→59.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.518 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 7041 4 %RANDOM
Rwork0.171 ---
obs0.172 169354 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.39→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5853 0 32 959 6844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225994
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9558156
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94324.368261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86715970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9411542
X-RAY DIFFRACTIONr_chiral_restr0.1040.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024545
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.22939
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2702
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.2197
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.121.53916
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67226121
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.43732363
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6354.52035
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: 1.39→1.43 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.258 513
Rwork0.257 12410
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)
10.63460.10610.16960.6476-0.38190.88070.0583-0.0738-0.066-0.0221-0.01270.06340.1507-0.1033-0.0456-0.0038-0.04070.0092-0.01360.0014-0.021853.49650.94475.396
21.4396-1.22010.93082.819-2.39122.4190.12640.0025-0.0642-0.17790.07930.27260.2505-0.2656-0.2058-0.05460.0007-0.02530.02420.010.008841.57768.52655.391
30.3581-0.1553-0.24860.76680.1940.49860.01010.0567-0.0741-0.0913-0.09970.03780.1594-0.00430.08950.05790.04840.0014-0.0159-0.0196-0.032867.78846.85144.654
41.97581.7058-0.41132.836-0.06680.89660.0066-0.0175-0.2044-0.2616-0.1286-0.33630.04140.17650.122-0.00920.06990.0680.03510.0676-0.016988.92466.56940.398
50.1719-0.19740.04060.9396-0.27420.72940.02030.00730.00510.063-0.1106-0.11630.1140.21690.0902-0.02510.0379-0.00480.03840.053-0.008787.35750.63672.461
60.8664-1.0361-0.15223.61221.94711.6646-0.0752-0.0662-0.01540.4254-0.0544-0.07910.08990.1130.12960.0609-0.0845-0.0339-0.00140.0172-0.062678.32573.05988.614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 237
2X-RAY DIFFRACTION2A238 - 256
3X-RAY DIFFRACTION3B1 - 237
4X-RAY DIFFRACTION4B238 - 256
5X-RAY DIFFRACTION5C1 - 237
6X-RAY DIFFRACTION6C238 - 256

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