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- PDB-6oxm: Crystal structure of L,L-diaminopimelate aminotransferase (DapL) ... -

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Basic information

Entry
Database: PDB / ID: 6oxm
TitleCrystal structure of L,L-diaminopimelate aminotransferase (DapL) from Verrucomicrobium spinosum
ComponentsDiaminopimelate aminotransferase
KeywordsTRANSFERASE / diaminopimelate aminotransferase / lysine biosynthesis
Function / homologyAspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesVerrucomicrobium spinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWeatherhead, A. / Meng, Y. / Dobson, R. / Hudson, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1120541 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM120653 United States
CitationJournal: To Be Published
Title: Characterization of Diaminopimelate Aminotransferase from Verrucomicrobium Spinosum
Authors: Weatherhead, A.W. / Meng, Y. / Dobson, R. / Hudson, A.
History
DepositionMay 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Diaminopimelate aminotransferase
B: Diaminopimelate aminotransferase


Theoretical massNumber of molelcules
Total (without water)89,8432
Polymers89,8432
Non-polymers00
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-31 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.050, 121.372, 76.545
Angle α, β, γ (deg.)90.00, 102.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 411 / Label seq-ID: 1 - 411

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Diaminopimelate aminotransferase


Mass: 44921.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucomicrobium spinosum (bacteria) / Plasmid: pET-30a (+) / Production host: Escherichia coli BL21 (bacteria) / References: LL-diaminopimelate aminotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% v/v T-mate, 100 mM malic acid

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 2.25→49.46 Å / Num. obs: 44544 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.926 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.092 / Rrim(I) all: 0.172 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.383.51.3341589644790.3350.8431.5831.995.7
8.59-49.463.60.04431808900.9960.0270.05120.399.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
Coot0.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QGU

3qgu


Resolution: 2.25→47.19 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 14.453 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2320 5 %RANDOM
Rwork0.18889 ---
obs0.19088 44427 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 38.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.11 Å2
2--0.07 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6215 0 0 460 6675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136351
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175792
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.6438610
X-RAY DIFFRACTIONr_angle_other_deg1.1591.57213426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08922.588340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.839151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2351540
X-RAY DIFFRACTIONr_chiral_restr0.050.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021366
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_it2.032.8283228
X-RAY DIFFRACTIONr_mcbond_other2.0292.8283227
X-RAY DIFFRACTIONr_mcangle_it3.3654.2354028
X-RAY DIFFRACTIONr_mcangle_other3.3654.2354029
X-RAY DIFFRACTIONr_scbond_it2.1243.0543123
X-RAY DIFFRACTIONr_scbond_other2.1243.0543124
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5094.4674583
X-RAY DIFFRACTIONr_long_range_B_refined6.0733.6126990
X-RAY DIFFRACTIONr_long_range_B_other6.05233.4376935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12730 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.254→2.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 159 -
Rwork0.281 3135 -
obs--94.79 %
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)
10.6386-0.2948-0.1170.69080.28760.4496-0.0157-0.1021-0.0280.10340.0195-0.03920.00960.0198-0.00380.128-0.00830.00840.02630.0090.01036.06116.1320.482
20.56190.1335-0.07511.03980.08640.5762-0.04770.01720.0014-0.00720.0168-0.086-0.02440.04160.03090.11780.01510.02590.0190.01030.01865.875-16.33121.173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 411
2X-RAY DIFFRACTION2B1 - 411

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