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- PDB-6n2h: Structure of D-ornithine/D-lysine decarboxylase from Salmonella t... -

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Basic information

Entry
Database: PDB / ID: 6n2h
TitleStructure of D-ornithine/D-lysine decarboxylase from Salmonella typhimurium
ComponentsD-ornithine/D-lysine decarboxylase
KeywordsLYASE / Pyridoxal-5'-phosphate / Fold III / decarboxylase / D-amino acid
Function / homology
Function and homology information


D-ornithine/D-lysine decarboxylase / diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate
Similarity search - Function
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
1,4-DIETHYLENE DIOXIDE / Diaminopimelate decarboxylase / D-ornithine/D-lysine decarboxylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsPhillips, R.S. / Hoover, T.R.
CitationJournal: Biochemistry / Year: 2019
Title: Crystal Structure of d-Ornithine/d-Lysine Decarboxylase, a Stereoinverting Decarboxylase: Implications for Substrate Specificity and Stereospecificity of Fold III Decarboxylases.
Authors: Phillips, R.S. / Poteh, P. / Krajcovic, D. / Miller, K.A. / Hoover, T.R.
History
DepositionNov 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-ornithine/D-lysine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9769
Polymers54,2911
Non-polymers6858
Water8,053447
1
A: D-ornithine/D-lysine decarboxylase
hetero molecules

A: D-ornithine/D-lysine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,95218
Polymers108,5822
Non-polymers1,37016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11750 Å2
ΔGint14 kcal/mol
Surface area32330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.740, 52.280, 86.700
Angle α, β, γ (deg.)90.000, 127.600, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein D-ornithine/D-lysine decarboxylase


Mass: 54291.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: DD95_01965 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D6FAR3, UniProt: Q8ZNC4*PLUS
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.05 M potassium phosphate, pH 7, 28-30% dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→46.88 Å / Num. obs: 50643 / % possible obs: 99.94 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.18 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1628 / Rpim(I) all: 0.06693 / Rrim(I) all: 0.1763 / Net I/σ(I): 6.92
Reflection shellResolution: 1.72→1.782 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.555 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 5022 / CC1/2: 0.247 / Rpim(I) all: 1.044 / Rrim(I) all: 2.764 / % possible all: 99.82

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGH

2qgh


Resolution: 1.72→46.88 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.38
RfactorNum. reflection% reflection
Rfree0.1926 2002 3.95 %
Rwork0.1636 --
obs0.1647 50623 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.95 Å2 / Biso mean: 35.7397 Å2 / Biso min: 16.91 Å2
Refinement stepCycle: final / Resolution: 1.72→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 104 447 4225
Biso mean--87.06 43.48 -
Num. residues----459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.72-1.7630.43271380.368634233561
1.763-1.81060.34951390.336834973636
1.8106-1.86390.32031440.296834193563
1.8639-1.92410.2741360.244234593595
1.9241-1.99280.25271500.209634413591
1.9928-2.07260.22171390.193334633602
2.0726-2.1670.20511440.179734543598
2.167-2.28120.21141420.151834523594
2.2812-2.42410.19741430.149934803623
2.4241-2.61130.1881420.146834733615
2.6113-2.8740.20231510.152234813632
2.874-3.28980.17791410.144634843625
3.2898-4.14440.18231390.128635123651
4.1444-46.90140.1421540.151635833737
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)
13.1072-0.09930.34443.57510.41742.10240.0137-0.29710.070.2505-0.09220.1064-0.0931-0.31850.0650.24610.01470.02450.3083-0.01280.158922.06346.751555.1967
20.3580.00220.26120.3911-0.10871.36540.0233-0.009-0.0732-0.03310.01430.03490.084-0.1165-0.03150.2229-0.0152-0.00290.2346-0.00980.250420.034-3.510625.8561
32.8370.45080.88125.63630.58572.72490.13620.20170.2284-0.0578-0.2084-0.0722-0.15990.05450.05220.21070.03690.04470.28840.01350.189326.25355.41947.2121
42.0455-0.41940.75540.99030.2583.10650.0188-0.0370.1172-0.0651-0.02560.034-0.4472-0.22430.06370.24340.03770.02190.27320.01290.23716.690610.963813.1601
51.36540.06991.23530.90251.02395.4682-0.1287-0.08210.1627-0.0633-0.00150.0147-0.7117-0.17260.31450.32460.0531-0.00580.2481-0.00490.287718.49614.813931.1895
62.1846-0.3252.44680.2276-0.27244.0161-0.0575-0.01330.0650.00140.02310.0121-0.1787-0.11330.05940.20060.01080.03480.1997-0.00920.224920.17668.730233.8514
72.97170.5140.64751.27650.17021.8871-0.0183-0.10130.2530.0753-0.0152-0.1166-0.36620.11790.03040.2565-0.006-0.00820.1739-0.02050.220437.130112.794652.3731
80.8603-0.2087-0.01890.88180.38121.07780.0154-0.08670.00270.01430.0051-0.0331-0.0301-0.01-0.01830.2036-0.01230.00660.20050.01820.201736.19770.524245.753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 146 )A48 - 146
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 206 )A147 - 206
4X-RAY DIFFRACTION4chain 'A' and (resid 207 through 247 )A207 - 247
5X-RAY DIFFRACTION5chain 'A' and (resid 248 through 283 )A248 - 283
6X-RAY DIFFRACTION6chain 'A' and (resid 284 through 331 )A284 - 331
7X-RAY DIFFRACTION7chain 'A' and (resid 332 through 377 )A332 - 377
8X-RAY DIFFRACTION8chain 'A' and (resid 378 through 466 )A378 - 466

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