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- PDB-3c0j: Structure of E. coli dihydrodipicolinate synthase complexed with ... -

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Basic information

Entry
Database: PDB / ID: 3c0j
TitleStructure of E. coli dihydrodipicolinate synthase complexed with hydroxypyruvate
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / dihydrodipicolinate synthase / lysine biosynthase / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Lysine biosynthesis / Schiff base
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / identical protein binding / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDobson, R.C.J.
CitationJournal: Protein Sci. / Year: 2008
Title: Conserved main-chain peptide distortions: A proposed role for Ile203 in catalysis by dihydrodipicolinate synthase
Authors: Dobson, R.C.J. / Griffin, M.D.W. / Devenish, S.R.A. / Pearce, F.G. / Hutton, C.A. / Gerrard, J.A. / Jameson, G.B. / Perugini, M.A.
History
DepositionJan 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3249
Polymers62,7802
Non-polymers5447
Water8,377465
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules

A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,64918
Polymers125,5604
Non-polymers1,08914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-27 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.967, 120.967, 110.639
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Dihydrodipicolinate synthase / DHDPS


Mass: 31389.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dapA / Plasmid: pJG001 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P0A6L2, dihydrodipicolinate synthase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.73 Å3/Da / Density % sol: 67.04 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 1.8M K2HPO4 (pH 10.0), 6% w/v N-octyl-D-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→34.79 Å / Num. all: 36400 / Num. obs: 36400 / % possible obs: 98.5 % / Redundancy: 3.96 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.8 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YXC

1yxc


Resolution: 2.4→31.49 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.465 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23729 1818 5 %RANDOM
Rwork0.1702 ---
obs0.1734 34563 100 %-
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: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.17 Å20 Å2
2---0.35 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.4→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 30 465 4855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224502
X-RAY DIFFRACTIONr_bond_other_d0.0020.022931
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9766129
X-RAY DIFFRACTIONr_angle_other_deg1.09537225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0415595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61924.514175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41215742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.221526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02822
X-RAY DIFFRACTIONr_nbd_refined0.2220.21010
X-RAY DIFFRACTIONr_nbd_other0.2050.23199
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22203
X-RAY DIFFRACTIONr_nbtor_other0.0930.22246
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2350
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1480.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7891.52921
X-RAY DIFFRACTIONr_mcbond_other0.1821.51193
X-RAY DIFFRACTIONr_mcangle_it1.47124719
X-RAY DIFFRACTIONr_scbond_it2.67431591
X-RAY DIFFRACTIONr_scangle_it4.124.51403
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 183 -
Rwork0.221 2478 -
obs--100 %

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