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- PDB-4xky: Structure of dihydrodipicolinate synthase from the commensal bact... -

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Basic information

Entry
Database: PDB / ID: 4xky
TitleStructure of dihydrodipicolinate synthase from the commensal bacterium Bacteroides thetaiotaomicron at 2.1 A resolution
Components(Dihydrodipicolinate synthase) x 2
KeywordsLYASE / Dihydrodipicolinate Synthase / Diaminopimelate / Lysine / Tetramer / Aldolase
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / cytosol
Similarity search - Function
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
ACETATE ION / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMank, N.J. / Arnette, A.K. / Klapper, V.G. / Chruszcz, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of dihydrodipicolinate synthase from the commensal bacterium Bacteroides thetaiotaomicron at 2.1 angstrom resolution.
Authors: Mank, N. / Arnette, A. / Klapper, V. / Offermann, L. / Chruszcz, M.
History
DepositionJan 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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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)131,3106
Polymers131,2284
Non-polymers822
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-81 kcal/mol
Surface area41720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.903, 91.988, 208.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydrodipicolinate synthase


Mass: 32818.891 Da / Num. of mol.: 1 / Fragment: UNP residues 5-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2814 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A3Z0
#2: Protein Dihydrodipicolinate synthase


Mass: 32802.891 Da / Num. of mol.: 3 / Fragment: UNP residues 5-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2814 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A3Z0
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.44 % / Description: Rod like
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8 M Sodium Chloride, 0.1 M Succinate pH 7, 0.1 M Acetate pH 4.6, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Aug 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 76582 / % possible obs: 99.8 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.034 / Rrim(I) all: 0.097 / Χ2: 0.87 / Net I/av σ(I): 25.417 / Net I/σ(I): 6 / Num. measured all: 616664
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.148.30.71837590.8740.2640.7650.517100
2.14-2.188.30.59237740.9110.2170.6310.535100
2.18-2.228.30.52637910.9240.1930.5610.558100
2.22-2.266.10.62737800.8510.260.681.76299.4
2.26-2.3180.4337440.9470.1610.4590.647100
2.31-2.378.30.31538120.9660.1150.3360.611100
2.37-2.428.40.27838290.9710.1020.2970.615100
2.42-2.498.40.23537680.9790.0860.2510.641100
2.49-2.568.30.22337840.9820.0820.2370.682100
2.56-2.658.20.19738310.9830.0730.210.737100
2.65-2.748.10.20138080.980.0760.2141.01100
2.74-2.858.30.13938280.9920.0510.1480.776100
2.85-2.988.40.11538020.9930.0420.1220.81100
2.98-3.148.30.09338270.9950.0340.0990.83100
3.14-3.338.30.07638350.9970.0280.0810.833100
3.33-3.597.90.07638760.9970.0290.0811.194100
3.59-3.9570.08137630.9960.0320.0871.78997.5
3.95-4.528.10.05238970.9980.0190.0561.30799.9
4.52-5.78.10.04539510.9990.0170.0481.031100
5.7-507.70.03741230.9980.0140.0390.95699.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22054 3846 5 %RANDOM
Rwork0.18463 ---
obs0.18647 72649 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.834 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0 Å2
2--1.62 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9080 0 5 515 9600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199387
X-RAY DIFFRACTIONr_bond_other_d00.029043
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.98412784
X-RAY DIFFRACTIONr_angle_other_deg3.625320834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36451217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.46224.744371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.474151540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4971536
X-RAY DIFFRACTIONr_chiral_restr0.0880.21474
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110700
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022018
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_it1.9412.624845
X-RAY DIFFRACTIONr_mcbond_other1.942.624843
X-RAY DIFFRACTIONr_mcangle_it3.2233.9176066
X-RAY DIFFRACTIONr_mcangle_other3.2233.9186067
X-RAY DIFFRACTIONr_scbond_it2.2712.8864542
X-RAY DIFFRACTIONr_scbond_other2.2712.8874543
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7834.2336718
X-RAY DIFFRACTIONr_long_range_B_refined6.88121.810984
X-RAY DIFFRACTIONr_long_range_B_other6.85921.59510855
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 245 -
Rwork0.215 4877 -
obs--90.83 %
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)
10.757-0.0987-0.06790.5572-0.00191.4906-0.0352-0.07460.01240.14190.0332-0.1063-0.1581-0.00210.00190.0978-0.0078-0.07020.0202-0.01030.170914.78618.588-26.838
21.0349-0.17960.2330.4907-0.30680.3957-0.01440.0033-0.0214-0.03590.0034-0.05270.00450.05250.01110.00540.00190.00150.07360.00430.183122.237-11.399-45.425
31.02470.19440.06721.7764-0.13471.1381-0.02070.03160.06270.4595-0.00580.1511-0.0002-0.04420.02640.17430.04150.04180.0515-0.00750.055-3.53-1.302-4.152
40.64030.0685-0.10150.4615-0.20140.93910.0026-0.0585-0.0480.0754-0.0222-0.01650.0334-0.01190.01960.01960.0018-0.00720.03470.01360.1818-3.9-27.494-28.697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 299
2X-RAY DIFFRACTION2B1 - 298
3X-RAY DIFFRACTION3C1 - 299
4X-RAY DIFFRACTION4D1 - 300

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