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- PDB-2v82: KDPGal complexed to KDPGal -

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Basic information

Entry
Database: PDB / ID: 2v82
TitleKDPGal complexed to KDPGal
Components2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE ALDOLASE
KeywordsLYASE / KDPGAL / ALDOLASE
Function / homology
Function and homology information


2-dehydro-3-deoxy-6-phosphogalactonate aldolase / D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity
Similarity search - Function
KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-KETO-DEOXY-GALACTOSE / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNaismith, J.H.
CitationJournal: Bioorg. Med. Chem. / Year: 2008
Title: Characterization and crystal structure of Escherichia coli KDPGal aldolase.
Authors: Walters, M.J. / Srikannathasan, V. / McEwan, A.R. / Naismith, J.H. / Fierke, C.A. / Toone, E.J.
History
DepositionAug 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
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 / 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7472
Polymers22,4891
Non-polymers2581
Water1,09961
1
A: 2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE ALDOLASE
hetero molecules

A: 2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE ALDOLASE
hetero molecules

A: 2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2426
Polymers67,4683
Non-polymers7743
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3670 Å2
ΔGint-37.1 kcal/mol
Surface area28470 Å2
MethodPQS
Unit cell
Length a, b, c (Å)104.600, 104.600, 74.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2029-

HOH

21A-2036-

HOH

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Components

#1: Protein 2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE ALDOLASE / 6-PHOSPHO-2-DEHYDRO-3-DEOXYGALACTONATE ALDOLASE / 2-OXO-3-DEOXYGALACTONATE 6-PHOSPHATE ALDOLASE


Mass: 22489.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q6BF16, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
#2: Chemical ChemComp-KDP / 2-KETO-DEOXY-GALACTOSE


Mass: 258.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details2 KETO DEOXY GALACTOSE (KDP): COVALENT LINKAGE WITH A LYS 126

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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: 3.52 Å3/Da / Density % sol: 64.81 % / Description: NONE
Crystal growpH: 6 / Details: pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 17654 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V81

2v81


Resolution: 2.1→52.27 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.321 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 863 4.9 %RANDOM
Rwork0.215 ---
obs0.216 16789 99.9 %-
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: 35.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→52.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 15 61 1581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221554
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9742125
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6185206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.824.82858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88715233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.925157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021180
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2778
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21084
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7631.51042
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99821630
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6023581
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4634.5494
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 76
Rwork0.244 1226
Refinement TLS params.Method: refined / Origin x: 18.099 Å / Origin y: 8.525 Å / Origin z: 0.031 Å
111213212223313233
T-0.0774 Å2-0.0063 Å20.0055 Å2--0.1554 Å2-0.0341 Å2---0.1018 Å2
L3.7989 °2-0.4275 °2-0.674 °2-0.799 °2-0.1894 °2--1.1134 °2
S0.1159 Å °0.0478 Å °0.3593 Å °-0.0655 Å °-0.0109 Å °0.0379 Å °-0.184 Å °0.0794 Å °-0.105 Å °

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