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- PDB-7jpj: Crystal Structure of the essential dimeric LYSA from Phaeodactylu... -

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Basic information

Entry
Database: PDB / ID: 7jpj
TitleCrystal Structure of the essential dimeric LYSA from Phaeodactylum tricornutum
ComponentsDiaminopimelate decarboxylase
KeywordsLYASE / PLP BINDING ENZYME / DECARBOXYLASE / LYSINE BIOSYNTHESIS / D-LYSINE / OBLIGATE DIMER / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate
Similarity search - Function
Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
D-LYSINE / Diaminopimelate decarboxylase
Similarity search - Component
Biological speciesPhaeodactylum tricornutum (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.78 Å
AuthorsFedorov, E. / Belinski, V.A. / Brunson, J.K. / Almo, S.C. / Dupont, C.L. / Ghosh, A.
CitationJournal: Biorxiv / Year: 2020
Title: The Phaeodactylum tricornutum diaminopimelate decarboxylase was acquired via horizontal gene transfer from bacteria and displays substrate promiscuity
Authors: Bielinski, V.A. / Brunson, J.K. / Ghosh, A. / Moosburner, M.A. / Garza, E.A. / Fussy, Z. / Bai, J. / McKinnie, S.M.K. / Moore, B.S. / Allen, A.E. / Almo, S.C. / Dupont, C.L.
History
DepositionAug 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diaminopimelate decarboxylase
B: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,58210
Polymers93,7632
Non-polymers8198
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-131 kcal/mol
Surface area30200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.780, 86.324, 127.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diaminopimelate decarboxylase /


Mass: 46881.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeodactylum tricornutum (Diatom) / Strain: CCAP 1055/1 / Gene: PHATRDRAFT_21592 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7G3A2
#2: Chemical ChemComp-DLY / D-LYSINE / Lysine


Type: D-peptide linking / Mass: 146.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.11 % / Description: Rectangular
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.0 M Ammonium sulfate and 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 25, 2020
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.78→19.88 Å / Num. obs: 24364 / % possible obs: 99.3 % / Redundancy: 13.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.274 / Rpim(I) all: 0.077 / Rrim(I) all: 0.285 / Net I/σ(I): 9.5 / Num. measured all: 328037
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
2.78-2.9313.50.8544578833900.8950.2380.8873.496.7
8.78-19.8812.80.093100537880.9970.0270.09720.291.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.66 Å29.73 Å
Translation2.66 Å29.73 Å

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Processing

Software
NameVersionClassification
PHENIXdev_3940refinement
XDSFAST_DPdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNW

1knw


Resolution: 2.78→18.99 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2415 1307 5.38 %
Rwork0.1965 22992 -
obs0.1989 24299 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.29 Å2 / Biso mean: 23.4729 Å2 / Biso min: 12.26 Å2
Refinement stepCycle: final / Resolution: 2.78→18.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6448 0 58 49 6555
Biso mean--34.96 19.59 -
Num. residues----864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036631
X-RAY DIFFRACTIONf_angle_d0.548987
X-RAY DIFFRACTIONf_dihedral_angle_d4.851922
X-RAY DIFFRACTIONf_chiral_restr0.0431009
X-RAY DIFFRACTIONf_plane_restr0.0041175
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.78-2.890.31281410.25792414255596
2.89-3.020.31631550.256624892644100
3.02-3.180.27751480.244525242672100
3.18-3.370.28471400.220125502690100
3.37-3.630.25581150.200225742689100
3.63-3.990.23821460.187225622708100
3.99-4.560.2151400.160125832723100
4.57-5.720.2181430.171426192762100
5.73-18.990.18151790.169526772856100
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)
10.9269-0.85770.00330.8861-0.31590.58070.28910.09110.002-0.2151-0.2210.03410.23950.12940.01510.17640.0545-0.02730.12410.00290.197428.40743.21124.448
22.33520.22010.8121.4191-0.73762.18360.13410.29920.2541-0.2152-0.3054-0.08630.15790.27060.22060.18110.03530.02220.08130.0260.141517.24557.55128.278
30.58410.41250.1310.4107-0.17841.52160.02310.04130.17070.087-0.1683-0.0952-0.4425-0.25570.12930.27090.0062-0.01520.11220.00470.241816.51164.1638.282
42.8804-1.1247-0.27212.0102-0.62183.9145-0.0488-0.1307-0.2867-0.158-0.08520.50370.1719-0.56250.11790.260.1429-0.0370.2462-0.03180.25681.05559.88341.969
52.1634-1.4333-0.62011.5151-0.40422.2597-0.03720.0247-0.12460.0253-0.02220.37930.0136-0.40030.03040.15920.0133-0.00740.2021-0.00020.2484-2.13457.09535.325
62.1154-1.96630.82282.3436-1.13621.23250.17140.0552-0.0791-0.2232-0.09440.12770.1240.0167-0.07670.1333-0.00930.02140.104-0.04880.210215.51440.94830.764
70.959-0.0478-0.20682.183-0.65051.8887-0.0170.0637-0.0505-0.0802-0.04660.13790.2375-0.05780.03450.1066-0.0051-0.02620.1646-0.01150.169727.34131.07335.978
80.9065-0.80650.50531.3554-0.73690.8748-0.1452-0.2209-0.06820.20660.13980.0783-0.1653-0.05250.03070.15840.023-0.00540.1657-0.0120.184624.68143.90169.18
90.8892-0.85280.21882.30580.22681.79860.0295-0.10380.1545-0.031-0.1126-0.3197-0.10940.30540.03970.1245-0.02980.01970.19540.01820.178441.72536.62657.872
100.58750.6174-0.04112.06290.72971.37270.01470.0281-0.1245-0.0330.06990.56120.3208-0.22410.13220.1313-0.1453-0.05570.0354-0.02640.32342.73627.91756.519
112.67533.49161.44998.9433-0.97692.663-0.2617-0.17930.1526-0.61870.3129-0.27540.09420.29970.16760.10130.03570.06930.1548-0.00940.278842.71221.88546.586
121.1372-0.69160.1480.9901-0.64310.73960.0190.0025-0.21520.0499-0.04510.04410.30870.00050.00530.154-0.0074-0.03530.12210.00850.239132.40921.36560.885
132.1345-1.70840.1572.4973-0.63451.37610.15180.1846-0.0642-0.03610.0960.1120.1089-0.3551-0.2020.18940.055-0.00470.23980.02790.16326.4647.69154.208
142.3059-0.69720.32892.03640.47511.0958-0.0985-0.0496-0.00440.23850.0853-0.0159-0.0799-0.27690.04620.1780.03720.02220.20260.04080.14958.63148.3157.848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 39:83 )A39 - 83
2X-RAY DIFFRACTION2( CHAIN A AND RESID 84:107 )A84 - 107
3X-RAY DIFFRACTION3( CHAIN A AND RESID 108:150 )A108 - 150
4X-RAY DIFFRACTION4( CHAIN A AND RESID 151:199 )A151 - 199
5X-RAY DIFFRACTION5( CHAIN A AND RESID 200:278 )A200 - 278
6X-RAY DIFFRACTION6( CHAIN A AND RESID 279:369 )A279 - 369
7X-RAY DIFFRACTION7( CHAIN A AND RESID 370:439 )A370 - 439
8X-RAY DIFFRACTION8( CHAIN B AND RESID 39:106 )B39 - 106
9X-RAY DIFFRACTION9( CHAIN B AND RESID 107:151 )B107 - 151
10X-RAY DIFFRACTION10( CHAIN B AND RESID 152:158 )B152 - 158
11X-RAY DIFFRACTION11( CHAIN B AND RESID 159:164 )B159 - 164
12X-RAY DIFFRACTION12( CHAIN B AND RESID 165:330 )B165 - 330
13X-RAY DIFFRACTION13( CHAIN B AND RESID 331:369 )B331 - 369
14X-RAY DIFFRACTION14( CHAIN B AND RESID 370:439 )B370 - 439

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