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- PDB-3n2o: X-ray crystal structure of arginine decarboxylase complexed with ... -

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Basic information

Entry
Database: PDB / ID: 3n2o
TitleX-ray crystal structure of arginine decarboxylase complexed with Arginine from Vibrio vulnificus
ComponentsBiosynthetic arginine decarboxylase
KeywordsLYASE
Function / homology
Function and homology information


arginine decarboxylase / arginine decarboxylase activity / spermidine biosynthetic process / arginine catabolic process / metal ion binding
Similarity search - Function
Helix Hairpins - #3440 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #930 / Arginine decarboxylase / Arginine decarboxylase, helical bundle domain / Arginine decarboxylase, C-terminal helical / Arginine decarboxylase helical bundle domain / Arginine decarboxylase C-terminal helical extension / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain ...Helix Hairpins - #3440 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #930 / Arginine decarboxylase / Arginine decarboxylase, helical bundle domain / Arginine decarboxylase, C-terminal helical / Arginine decarboxylase helical bundle domain / Arginine decarboxylase C-terminal helical extension / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix Hairpins / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AGMATINE / PYRIDOXAL-5'-PHOSPHATE / Biosynthetic arginine decarboxylase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsDeng, X. / Lee, J. / Michael, A.J. / Tomchick, D.R. / Goldsmith, E.J. / Phillips, M.A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine ...Title: Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine.
Authors: Deng, X. / Lee, J. / Michael, A.J. / Tomchick, D.R. / Goldsmith, E.J. / Phillips, M.A.
History
DepositionMay 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 22, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biosynthetic arginine decarboxylase
B: Biosynthetic arginine decarboxylase
C: Biosynthetic arginine decarboxylase
D: Biosynthetic arginine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,06812
Polymers294,5594
Non-polymers1,5098
Water7,981443
1
A: Biosynthetic arginine decarboxylase
B: Biosynthetic arginine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,0346
Polymers147,2792
Non-polymers7554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-64 kcal/mol
Surface area46670 Å2
MethodPISA
2
C: Biosynthetic arginine decarboxylase
D: Biosynthetic arginine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,0346
Polymers147,2792
Non-polymers7554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-64 kcal/mol
Surface area46470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.648, 119.365, 121.840
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
Biosynthetic arginine decarboxylase / ADC


Mass: 73639.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: YJ016 / Gene: ADC, speA, VV1986 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7MK24, arginine decarboxylase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H14N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 0.2 M MgCl2, 12% PEG 4000., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2009
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator.
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.3→121.1 Å / Num. all: 128263 / Num. obs: 127349 / % possible obs: 98.8 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 17.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXDphasing
REFMAC5.5.0072refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→121.1 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 15.247 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.1 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23921 6366 5 %RANDOM
Rwork0.17878 ---
all0.1962 128263 --
obs0.18182 127349 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å21.9 Å2
2---0.49 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→121.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20053 0 96 443 20592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02220533
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.95627832
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75652512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32724.7171060
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.219153526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.20315136
X-RAY DIFFRACTIONr_chiral_restr0.1220.23075
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115748
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0321.512492
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.007220140
X-RAY DIFFRACTIONr_scbond_it3.49438041
X-RAY DIFFRACTIONr_scangle_it5.4214.57692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A5005medium positional0.360.5
22B4997medium positional0.520.5
11A5005medium thermal1.32
22B4997medium thermal1.132
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 439 -
Rwork0.249 7954 -
obs--89.04 %
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)
10.08560.0246-0.05320.21260.07260.25770.0235-0.0079-0.03020.0913-0.0079-0.05580.04330.0103-0.01550.05950.0071-0.01280.01590.01140.040914.145731.072147.2305
20.03050.05510.00580.11870.04510.15530.00950.0146-0.00250.0270.01240.0072-0.009-0.0253-0.02190.02180.00980.02180.02990.00080.0315-3.762339.727532.2098
30.07370.06750.05560.20370.02990.1699-0.01050.01350.00240.01310.0026-0.0305-0.03190.01060.00790.0174-0.00460.01160.04010.01210.045228.832673.941318.5555
40.08890.0646-0.01250.15170.03680.1568-0.01140.009-0.05160.0036-0.0007-0.09030.01820.05560.01220.00770.00830.01250.05420.01160.088445.425755.611917.8681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 639
2X-RAY DIFFRACTION1A1001
3X-RAY DIFFRACTION1B1002
4X-RAY DIFFRACTION2B11 - 638
5X-RAY DIFFRACTION2B1001
6X-RAY DIFFRACTION2A1002
7X-RAY DIFFRACTION3C12 - 638
8X-RAY DIFFRACTION3C1001
9X-RAY DIFFRACTION3C1002
10X-RAY DIFFRACTION4D11 - 638
11X-RAY DIFFRACTION4D1001
12X-RAY DIFFRACTION4D1002

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