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- PDB-3flu: Crystal structure of dihydrodipicolinate synthase from the pathog... -

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Basic information

Entry
Database: PDB / ID: 3flu
TitleCrystal structure of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / TIM barrel / beta-alpha-barrel / 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 / cytoplasm
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 speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDevenish, S.R.A. / Hadfield, A.T.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis.
Authors: Devenish, S.R.A. / Huisman, F.H.A. / Parker, E.J. / Hadfield, A.T. / Gerrard, J.A.
History
DepositionDec 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
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_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)130,56051
Polymers126,1604
Non-polymers4,40047
Water16,898938
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-381 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.667, 115.684, 132.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNMETMETDD3 - 139 - 19
21GLNGLNMETMETAA3 - 139 - 19
31GLNGLNMETMETBB3 - 139 - 19
41GLNGLNMETMETCC3 - 139 - 19
12ILEILEVALVALDD28 - 6334 - 69
22ILEILEVALVALAA28 - 6334 - 69
32ILEILEVALVALBB28 - 6334 - 69
42ILEILEVALVALCC28 - 6334 - 69
13VALVALTHRTHRDD67 - 8273 - 88
23VALVALTHRTHRAA67 - 8273 - 88
33VALVALTHRTHRBB67 - 8273 - 88
43VALVALTHRTHRCC67 - 8273 - 88
14ILEILETHRTHRDD86 - 14492 - 150
24ILEILETHRTHRAA86 - 14492 - 150
34ILEILETHRTHRBB86 - 14492 - 150
44ILEILETHRTHRCC86 - 14492 - 150
15PROPROILEILEDD155 - 174161 - 180
25PROPROILEILEAA155 - 174161 - 180
35PROPROILEILEBB155 - 174161 - 180
45PROPROILEILECC155 - 174161 - 180
16PHEPHELEULEUDD181 - 228187 - 234
26PHEPHELEULEUAA181 - 228187 - 234
36PHEPHELEULEUBB181 - 228187 - 234
46PHEPHELEULEUCC181 - 228187 - 234
17ILEILEARGARGDD237 - 261243 - 267
27ILEILEARGARGAA237 - 261243 - 267
37ILEILEARGARGBB237 - 261243 - 267
47ILEILEARGARGCC237 - 261243 - 267
18ARGARGLEULEUDD267 - 273273 - 279
28ARGARGLEULEUAA267 - 273273 - 279
38ARGARGLEULEUBB267 - 273273 - 279
48ARGARGLEULEUCC267 - 273273 - 279
19GLYGLYGLNGLNDD277 - 290283 - 296
29GLYGLYGLNGLNAA277 - 290283 - 296
39GLYGLYGLNGLNBB277 - 290283 - 296
49GLYGLYGLNGLNCC277 - 290283 - 296

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Components

#1: Protein
Dihydrodipicolinate synthase / DHDPS


Mass: 31540.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: Serogroup B / Gene: dapA, NMB0929 / Plasmid: pET-151/D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: Q9JZR4, dihydrodipicolinate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 938 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 1.8M ammonium sulfate, 100mM Bis-Tris.HCl, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2008
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.999→115.684 Å / Num. all: 84335 / Num. obs: 84251 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.23 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.349 / Num. unique all: 8359 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.16 Å
Translation2.5 Å41.16 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YXC

1yxc


Resolution: 2→115.47 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.158 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.887 / SU B: 3.03 / SU ML: 0.086 / SU R Cruickshank DPI: 0.152 / SU Rfree: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4201 5 %RANDOM
Rwork0.148 ---
obs0.151 84214 99.87 %-
all-84324 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.39 Å2 / Biso mean: 20.562 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.7 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→115.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8722 0 264 938 9924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229263
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.98812625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82551209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06524.793363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.642151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8031549
X-RAY DIFFRACTIONr_chiral_restr0.090.21473
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026833
X-RAY DIFFRACTIONr_nbd_refined0.2130.24770
X-RAY DIFFRACTIONr_nbtor_refined0.3090.26376
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2799
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.229
X-RAY DIFFRACTIONr_mcbond_it1.72626087
X-RAY DIFFRACTIONr_mcangle_it2.25939543
X-RAY DIFFRACTIONr_scbond_it4.4214.53544
X-RAY DIFFRACTIONr_scangle_it6.21263060
Refine LS restraints NCS

Ens-ID: 1 / Number: 1719 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1DMEDIUM POSITIONAL0.21
2AMEDIUM POSITIONAL0.231
3BMEDIUM POSITIONAL0.251
4CMEDIUM POSITIONAL0.21
1DMEDIUM THERMAL1.742
2AMEDIUM THERMAL1.472
3BMEDIUM THERMAL1.522
4CMEDIUM THERMAL1.372
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 276 -
Rwork0.169 5813 -
all-6089 -
obs-5813 99.15 %

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