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- PDB-6t3t: Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from t... -

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Basic information

Entry
Database: PDB / ID: 6t3t
TitleStructure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / thermoacidophile / methanotrophy / 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. / 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 speciesMethylacidiphilum fumariolicum SolV (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSchmitz, R. / Dietl, A. / Mueller, M. / Berben, T. / Op den Camp, H. / Barends, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway.
Authors: Schmitz, R.A. / Dietl, A. / Muller, M. / Berben, T. / Op den Camp, H.J.M. / Barends, T.R.M.
History
DepositionOct 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / 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
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_asym_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)132,7298
Polymers132,3454
Non-polymers3844
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-142 kcal/mol
Surface area40480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.060, 109.060, 107.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11B-702-

HOH

21A-511-

HOH

31A-667-

HOH

41A-677-

HOH

51D-569-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))
21(chain B and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))
31(chain C and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))
41(chain D and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPHEPHE(chain A and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))AB2 - 1162 - 116
12HISHISGLYGLY(chain A and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))AB118 - 180118 - 180
13PHEPHEALAALA(chain A and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))AB182 - 301182 - 301
21LYSLYSPHEPHE(chain B and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))BA2 - 1162 - 116
22HISHISGLYGLY(chain B and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))BA118 - 180118 - 180
23PHEPHEALAALA(chain B and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))BA182 - 301182 - 301
31LYSLYSPHEPHE(chain C and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))CC2 - 1162 - 116
32HISHISGLYGLY(chain C and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))CC118 - 180118 - 180
33PHEPHEALAALA(chain C and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))CC182 - 301182 - 301
41LYSLYSPHEPHE(chain D and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))DD2 - 1162 - 116
42HISHISGLYGLY(chain D and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))DD118 - 180118 - 180
43PHEPHEALAALA(chain D and (resid 2 through 116 or resid 118 through 180 or resid 182 through 301))DD182 - 301182 - 301

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Components

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 33086.184 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Methylacidiphilum fumariolicum SolV (bacteria)
References: UniProt: I0JZ23, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M citric acid, 0.1 M lithium sulfate, 0.05 M sodium phosphate dibasic dihydrate, 19% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.773 Å / Num. obs: 74317 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 22.92 Å2 / Rrim(I) all: 0.156 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.15 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5359 / Rrim(I) all: 0.739

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YXG

2yxg


Resolution: 2.1→48.773 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.64
RfactorNum. reflection% reflection
Rfree0.2318 3740 5.1 %
Rwork0.1808 --
obs0.1836 73398 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.19 Å2 / Biso mean: 24.4192 Å2 / Biso min: 11.38 Å2
Refinement stepCycle: final / Resolution: 2.1→48.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9280 0 20 751 10051
Biso mean--35.15 31.15 -
Num. residues----1200
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3600X-RAY DIFFRACTION6.791TORSIONAL
12B3600X-RAY DIFFRACTION6.791TORSIONAL
13C3600X-RAY DIFFRACTION6.791TORSIONAL
14D3600X-RAY DIFFRACTION6.791TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12650.316620.2142262899
2.184-2.21520.26674360.21362308100
2.2834-2.32090.28494330.1982291100
2.4038-2.450.25723700.19982342100
2.5001-2.55440.25463870.19622353100
2.6138-2.67920.2531400.18772560100
2.6792-2.75160.24921710.19682551100
2.7516-2.83260.2755100.18422713100
2.8326-2.9240.24872840.1823240099
2.924-3.02850.22342580.18292491100
3.1497-3.29310.2342130.17862541100
3.2931-3.46660.20642010.17122504100
3.6838-3.96810.21151630.16032582100
3.9681-4.36720.21941570.15092591100
4.3672-4.99850.2082060.15122515100
4.9985-6.29550.22011580.19182599100

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