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- PDB-1yxd: Structure of E. coli dihydrodipicolinate synthase bound with allo... -

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Basic information

Entry
Database: PDB / ID: 1yxd
TitleStructure of E. coli dihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine to 2.0 A
Componentsdihydrodipicolinate synthase
KeywordsLYASE / dihydrodipicolinate synthase
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
: / LYSINE / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDobson, R.C.J. / Griffin, M.D.W. / Jameson, G.B. / Gerrard, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance.
Authors: Dobson, R.C. / Griffin, M.D. / Jameson, G.B. / Gerrard, J.A.
History
DepositionFeb 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,2019
Polymers62,6102
Non-polymers5917
Water10,034557
1
A: dihydrodipicolinate synthase
B: dihydrodipicolinate synthase
hetero molecules

A: dihydrodipicolinate synthase
B: dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,40118
Polymers125,2204
Non-polymers1,18114
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)121.148, 121.148, 110.084
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 /


Mass: 31304.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DapA / Plasmid: pBluescript +KS / 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 3.72 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 276 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 1.8M potassium phosphate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 276K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→37.99 Å / Num. obs: 63306 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.88 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.581 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18611 3225 5.1 %RANDOM
Rwork0.15933 ---
obs0.16074 60077 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: 19.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4321 0 34 557 4912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224418
X-RAY DIFFRACTIONr_bond_other_d0.0010.024159
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9576008
X-RAY DIFFRACTIONr_angle_other_deg0.90139635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1255582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84924.512164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37215721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0891523
X-RAY DIFFRACTIONr_chiral_restr0.1010.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02804
X-RAY DIFFRACTIONr_nbd_refined0.2330.2923
X-RAY DIFFRACTIONr_nbd_other0.1860.24056
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22226
X-RAY DIFFRACTIONr_nbtor_other0.0920.22288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2462
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.71.52914
X-RAY DIFFRACTIONr_mcbond_other0.1791.51204
X-RAY DIFFRACTIONr_mcangle_it1.30724694
X-RAY DIFFRACTIONr_scbond_it2.35731514
X-RAY DIFFRACTIONr_scangle_it3.7794.51314
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 219 -
Rwork0.205 4393 -
obs--100 %

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