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- PDB-7jzc: Dihydrodipicolinate synthase S48W mutant with lysine in the allos... -

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Basic information

Entry
Database: PDB / ID: 7jzc
TitleDihydrodipicolinate synthase S48W mutant with lysine in the allosteric site, and pyruvate in the catalytic site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / DHDPS / enzyme / allostery / lysine biosynthesis
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / 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-type TIM barrel
Similarity search - Domain/homology
: / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsBoard, A.J. / Dobson, R.C.J.
CitationJournal: To Be Published
Title: Mapping the uncharted water channel of DHDPS
Authors: Board, A.J. / Dobson, R.C.J.
History
DepositionSep 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0244
Polymers62,9462
Non-polymers782
Water4,990277
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0498
Polymers125,8924
Non-polymers1564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557-x,-x+y,-z+7/31
Unit cell
Length a, b, c (Å)121.129, 121.129, 111.271
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 4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 31473.104 Da / Num. of mol.: 2 / Mutation: S48W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: dapA, A6V01_06140, A8C65_04230, ACU57_04510, AM464_03890, AML07_10805, APZ14_05880, AUQ13_12840, AUS26_08890, AW106_01920, BANRA_01022, BANRA_04600, BMA87_04055, BUE81_00170, BvCms2454_00575, ...Gene: dapA, A6V01_06140, A8C65_04230, ACU57_04510, AM464_03890, AML07_10805, APZ14_05880, AUQ13_12840, AUS26_08890, AW106_01920, BANRA_01022, BANRA_04600, BMA87_04055, BUE81_00170, BvCms2454_00575, BvCmsKSP026_00126, BvCmsSINP011_00590, BW690_08395, BZL31_19835, C5N07_10510, C9306_12515, C9Z39_22035, C9Z89_01665, CG692_24655, CI693_08805, CIG45_08195, COD30_00655, D2185_06295, D3821_11825, D4638_04510, D4718_03620, D5H35_00590, D6004_00600, D9610_05430, D9D44_02140, D9I18_08280, D9J52_02245, D9S45_15015, DAH30_02905, DAH32_09095, DIV22_31750, DJ503_11770, DL326_03925, DL530_01595, DL800_18800, DLW60_01905, DMY83_09445, DNW42_05980, DQF71_00895, DS143_00895, DT034_06790, DTL43_01515, DVB38_05855, E2119_05140, E2134_09475, E2135_00560, E2855_03226, E2863_03133, E5P22_02280, E5S42_08940, EAI42_12285, EAI52_02575, EAM59_02025, EAN70_00660, EBM08_03910, EC3234A_44c00840, EC95NR1_01697, ECTO6_01408, ED307_17520, ED600_00625, EEP23_23010, EG599_00615, EH412_01980, EHJ36_02055, EI028_07440, EIZ93_19645, EKI52_22350, EL75_1173, EL79_1184, EL80_1189, EPT01_15155, ERS150876_00779, EYD11_06580, F1E19_01790, F7F00_00605, F7F23_09350, F7F26_01975, FQR64_06700, GHR40_11105, GKF74_08320, GKF86_10525, GKF89_17025, GP666_02180, GP935_11985, GQA06_13610, GQE30_13075, GQE34_24640, GQE51_05930, GRW80_06100, NCTC10963_01382, NCTC11126_06127, NCTC11341_00817, NCTC13216_00544, NCTC8960_04113, NCTC9045_01668, NCTC9062_01738, NCTC9962_06536, RK56_024520, SAMEA3472047_03904, SAMEA3484427_00338, SAMEA3484429_00447, SAMEA3752559_00798, SAMEA3753300_00971, SK85_02727
Production host: Escherichia coli (E. coli)
References: UniProt: A0A066Q637, 4-hydroxy-tetrahydrodipicolinate 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.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / Details: glucopyranoside, potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 294.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.82→33.34 Å / Num. obs: 57849 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.039 / Net I/σ(I): 17.5
Reflection shellResolution: 1.82→1.86 Å / Rmerge(I) obs: 0.329 / Num. unique obs: 4524 / Rpim(I) all: 0.156

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YXC

1yxc


Resolution: 2.07→39.65 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.483 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20861 2932 5.1 %RANDOM
Rwork0.1723 ---
obs0.17412 54898 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.966 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.07→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 2 277 4576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194419
X-RAY DIFFRACTIONr_bond_other_d0.0010.024274
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9636034
X-RAY DIFFRACTIONr_angle_other_deg0.95139785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9423.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83815694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3761527
X-RAY DIFFRACTIONr_chiral_restr0.1250.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02959
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.07→2.123 Å
RfactorNum. reflection% reflection
Rfree0.29 211 -
Rwork0.249 4021 -
obs--99.86 %

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