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- PDB-2a6l: Dihydrodipicolinate synthase (E. coli)- mutant R138H -

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Basic information

Entry
Database: PDB / ID: 2a6l
TitleDihydrodipicolinate synthase (E. coli)- mutant R138H
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / beta-alpha-barrel / dihydrodipicolinate synthase
Function / homology
Function and homology information


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / 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
: / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDobson, R.C. / Devenish, S.R. / Turner, L.A. / Clifford, V.R. / Pearce, F.G. / Jameson, G.B. / Gerrard, J.A.
CitationJournal: Biochemistry / Year: 2005
Title: Role of Arginine 138 in the Catalysis and Regulation of Escherichia coli Dihydrodipicolinate Synthase.
Authors: Dobson, R.C. / Devenish, S.R. / Turner, L.A. / Clifford, V.R. / Pearce, F.G. / Jameson, G.B. / Gerrard, J.A.
History
DepositionJul 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 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 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)62,6504
Polymers62,5722
Non-polymers782
Water9,620534
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules

A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,3008
Polymers125,1444
Non-polymers1564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)121.016, 121.016, 111.414
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-843-

HOH

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Components

#1: Protein Dihydrodipicolinate synthase / DHDPS


Mass: 31285.889 Da / Num. of mol.: 2 / Mutation: R138H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dapA / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 3.76 Å3/Da / Density % sol: 67.32 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 10
Details: protein solution (~5 mg/ml in Tris.HCl 20 mM, pH 8, 2.5 uL), precipitant (K2HPO4 1.8 M, pH 10, 1.2 uL), and N-octyl- -R-glucopyranoside (6% w/v, 0.6 uL), VAPOR DIFFUSION, temperature 12K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→33.3 Å / Num. obs: 59240 / % possible obs: 99.7 %
Reflection shellResolution: 2.05→33.3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 10.4 / Num. unique all: 59240 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→32.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.672 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2951 5 %RANDOM
Rwork0.18252 ---
obs0.184 56283 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: 23.345 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å20 Å2
2---0.25 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4323 0 2 534 4859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224395
X-RAY DIFFRACTIONr_bond_other_d0.0010.024113
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9495983
X-RAY DIFFRACTIONr_angle_other_deg0.79939535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76324.479163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34915722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6271522
X-RAY DIFFRACTIONr_chiral_restr0.0650.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024916
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02804
X-RAY DIFFRACTIONr_nbd_refined0.2130.2899
X-RAY DIFFRACTIONr_nbd_other0.1730.23967
X-RAY DIFFRACTIONr_nbtor_refined0.160.22211
X-RAY DIFFRACTIONr_nbtor_other0.0860.22199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2434
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3561.52900
X-RAY DIFFRACTIONr_mcbond_other0.0521.51192
X-RAY DIFFRACTIONr_mcangle_it0.68524676
X-RAY DIFFRACTIONr_scbond_it1.1131505
X-RAY DIFFRACTIONr_scangle_it1.874.51307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 183 -
Rwork0.263 4089 -
obs--100 %

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