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- PDB-3ler: Crystal Structure of Dihydrodipicolinate Synthase from Campylobac... -

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Basic information

Entry
Database: PDB / ID: 3ler
TitleCrystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / TIM barrel / Amino-acid biosynthesis / Cytoplasm / Diaminopimelate biosynthesis / Lysine biosynthesis / Schiff base / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
ACETIC ACID / FORMIC ACID / DI(HYDROXYETHYL)ETHER / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å
AuthorsKim, Y. / Zhou, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
Authors: Kim, Y. / Zhou, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0May 30, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity_poly / entity_poly_seq / pdbx_distant_solvent_atoms / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_validate_chiral / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.label_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id

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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
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,88210
Polymers133,5214
Non-polymers3616
Water19,8171100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-56 kcal/mol
Surface area40420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.185, 85.304, 199.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydrodipicolinate synthase / / DHDPS


Mass: 33380.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: dapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9PPB4, dihydrodipicolinate synthase

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Non-polymers , 6 types, 1106 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1100 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M NaCl, 0.1 M Na/K phosphate pH 6.2, 20% (w/v) PEG-1000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.84→39.21 Å / Num. all: 107674 / Num. obs: 107674 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.095 / Net I/σ(I): 9.1
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 5300 / Rsym value: 0.81 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84→39.207 Å / SU ML: 0.2 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 5343 4.99 %random
Rwork0.152 ---
all0.154 107116 --
obs0.154 107116 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.551 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.3289 Å20 Å20 Å2
2---0.1913 Å2-0 Å2
3----0.1376 Å2
Refinement stepCycle: LAST / Resolution: 1.84→39.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9340 0 23 1100 10463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139539
X-RAY DIFFRACTIONf_angle_d1.36912913
X-RAY DIFFRACTIONf_dihedral_angle_d19.1683582
X-RAY DIFFRACTIONf_chiral_restr0.0971481
X-RAY DIFFRACTIONf_plane_restr0.0071668
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.84-1.90580.23995190.18761008110600100
1.9058-1.98210.20885040.16181008010584100
1.9821-2.07230.20275160.15491013010646100
2.0723-2.18150.21165130.15491011810631100
2.1815-2.31820.20575610.14111007710638100
2.3182-2.49710.19465200.14631017810698100
2.4971-2.74840.19145350.14511018610721100
2.7484-3.14590.19195440.15451020810752100
3.1459-3.96290.16655280.14571026710795100
3.9629-39.21570.18326030.1493104481105198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35170.2208-0.38780.5018-0.00720.59590.1678-0.09930.14120.0222-0.0686-0.0376-0.17430.0786-0.09880.2236-0.0410.06270.1650.01010.184864.486620.9012166.1735
21.18960.0175-0.54440.5954-0.22080.9331-0.0977-0.0648-0.25940.0303-0.04810.02630.1179-0.06870.1320.162-0.02260.04220.14770.03280.215538.5502-15.6749187.8533
31.49760.2451-0.92120.3682-0.48271.32260.3288-0.03490.3670.1615-0.00750.1036-0.374-0.0289-0.30110.27430.00540.12410.1436-0.02230.244935.901821.8553185.1385
40.65530.1483-0.40250.31250.00520.9763-0.10510.0789-0.1983-0.0475-0.0503-0.08480.0995-0.06360.13580.16080.00430.05950.1456-0.03690.212255.8981-14.5439158.3216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 301
2X-RAY DIFFRACTION2chain BB1 - 303
3X-RAY DIFFRACTION3chain CC3 - 301
4X-RAY DIFFRACTION4chain DD1 - 301

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