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- PDB-3vab: Crystal structure of Diaminopimelate decarboxylase from Brucella ... -

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Basic information

Entry
Database: PDB / ID: 3vab
TitleCrystal structure of Diaminopimelate decarboxylase from Brucella melitensis bound to PLP
ComponentsDiaminopimelate decarboxylase 1
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / pyridoxal-phosphate / diaminopimelate decarboxylase / diaminopimelic acid decarboxylase / meso-diaminopimelate decarboxylase / DAP-decarboxylase / meso-2 / 6-diaminoheptanedioate carboxy-lyase / lysine biosynthesis
Function / homology
Function and homology information


diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate / pyridoxal phosphate binding
Similarity search - Function
Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / 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 ...Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / 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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Diaminopimelate decarboxylase
Similarity search - Component
Biological speciesBrucella melitensis bv. 1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Diaminopimelate decarboxylase from Brucella melitensis bound to PLP
Authors: Edwards, T.E. / Gardberg, A.S. / Letesson, J.J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 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

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Assembly

Deposited unit
A: Diaminopimelate decarboxylase 1
B: Diaminopimelate decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7266
Polymers96,4442
Non-polymers2824
Water13,061725
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-42 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.530, 126.370, 68.180
Angle α, β, γ (deg.)90.000, 112.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Diaminopimelate decarboxylase 1 / DAP decarboxylase 1 / DAPDC 1


Mass: 48221.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis bv. 1 (bacteria) / Strain: 16M / Gene: BMEI0084, lysA1 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YJJ9, diaminopimelate decarboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BrmeA.00771.a.A1 PS01273 at 36.9 mg/mL against JCSG+ E2 0.2 M sodium chloride, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate with 10 then 20% ethylene glycol as step cryo-protectant, ...Details: BrmeA.00771.a.A1 PS01273 at 36.9 mg/mL against JCSG+ E2 0.2 M sodium chloride, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate with 10 then 20% ethylene glycol as step cryo-protectant, crystal tracking ID 228027e2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 8, 2011 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 54306 / Num. obs: 53634 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 22.068 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.1-2.152.90.1745.97108784020376593.7
2.15-2.210.177.1513752385798.6
2.21-2.280.1697.4213332374298.6
2.28-2.350.1498.1613350364699.1
2.35-2.420.1328.8513080355099.4
2.42-2.510.1318.8812630342999.5
2.51-2.60.1219.3712299331699.3
2.6-2.710.1089.9411990322099.7
2.71-2.830.09710.6811491307199.8
2.83-2.970.08412.0611055294699.6
2.97-3.130.08112.5110466278099.6
3.13-3.320.07214.559878262699.4
3.32-3.550.05818.639250246999.2
3.55-3.830.05321.838374230199.2
3.83-4.20.048237768213198.7
4.2-4.70.04924.516822191598.6
4.7-5.420.05221.886341170098.7
5.42-6.640.05418.625462144599.4
6.64-9.390.04522.314166110699.3
9.390.03728.03218161996

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å44.7 Å
Translation3 Å44.7 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3n2b

3n2b


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.2429 / WRfactor Rwork: 0.2019 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8037 / SU B: 9.259 / SU ML: 0.153 / SU R Cruickshank DPI: 0.2709 / SU Rfree: 0.2158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 2737 5.1 %RANDOM
Rwork0.2212 ---
obs0.2236 53634 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.34 Å2 / Biso mean: 19.4125 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.6 Å2
2---0.85 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6388 0 17 725 7130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196620
X-RAY DIFFRACTIONr_bond_other_d0.0030.024431
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9799034
X-RAY DIFFRACTIONr_angle_other_deg1.105310807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77223.357283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.423151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6681552
X-RAY DIFFRACTIONr_chiral_restr0.0880.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217460
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021330
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 212 -
Rwork0.256 3497 -
all-3709 -
obs--93.8 %
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)
10.55660.02290.21880.8205-0.31910.2560.04440.00190.0496-0.207-0.0521-0.06060.12290.01450.00770.25570.0211-0.02120.1957-0.02560.1694-1.777512.54953.6537
20.321-0.21320.08130.54220.03880.0834-0.0148-0.01720.0383-0.07880.01970.03810.00450.0227-0.00490.20920.0081-0.00650.19630.00870.1938-7.804544.87097.6282
37.00822.20545.83550.69821.83974.86330.1755-0.2469-0.7752-0.05370.1938-0.2276-0.0793-0.1965-0.36930.86650.0018-0.09690.27510.01410.2938-21.008826.06495.8494
40.1721-0.06650.21650.3244-0.09810.27330.0256-0.0264-0.0255-0.05260.00060.00780.0406-0.0302-0.02620.1999-0.00190.00530.2007-0.00330.209-2.568518.807715.9959
50.0026-0.01160.01380.4197-0.02160.1379-0.0054-0.0064-0.0060.0247-0.0129-0.07370.00610.02570.01820.19440.0017-0.00910.20880.0020.215314.162519.499637.9006
60.188-0.1632-0.0590.96190.02120.446-0.0003-0.00470.02210.13240.01570.02640.0465-0.0277-0.01540.2066-0.00750.01380.18260.00760.20252.97957.215245.211
70.05510.4322-0.52593.5742-4.37035.34650.23870.00550.02980.91430.16310.3992-1.0919-0.0853-0.40190.6540.0443-0.21920.0524-0.06650.3723.555329.011352.5057
80.01120.00120.05520.3672-0.08220.32560.00880.00080.00770.0278-0.01720.0119-0.0345-0.00910.00840.1880.0070.01270.206-0.00380.21135.527736.259531.6036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 35
2X-RAY DIFFRACTION2A36 - 246
3X-RAY DIFFRACTION3A247 - 256
4X-RAY DIFFRACTION4A257 - 422
5X-RAY DIFFRACTION5B-3 - 161
6X-RAY DIFFRACTION6B162 - 246
7X-RAY DIFFRACTION7B247 - 256
8X-RAY DIFFRACTION8B257 - 422

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