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- PDB-2vyc: Crystal Structure of Acid Induced Arginine Decarboxylase from E. coli -

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Basic information

Entry
Database: PDB / ID: 2vyc
TitleCrystal Structure of Acid Induced Arginine Decarboxylase from E. coli
ComponentsBIODEGRADATIVE ARGININE DECARBOXYLASE
KeywordsLYASE / ARGININE DECARBOXYLASE / PYRIDOXAL PHOSPHATE / PLP-DEPENDENT ENZYME / DECARBOXYLASE / ACID RESISTANCE
Function / homology
Function and homology information


arginine decarboxylase / arginine decarboxylase activity / intracellular pH elevation / arginine catabolic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Ornithine Decarboxylase; Chain A, domain 4 / Orn/Lys/Arg decarboxylase, C-terminal domain / Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain ...Ornithine Decarboxylase; Chain A, domain 4 / Orn/Lys/Arg decarboxylase, C-terminal domain / Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Response regulator / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Biodegradative arginine decarboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.4 Å
AuthorsAndrell, J. / Hicks, M.G. / Palmer, T. / Carpenter, E.P. / Iwata, S. / Maher, M.J.
CitationJournal: Biochemistry / Year: 2009
Title: Crystal Structure of the Acid Induced Arginine Decarboxylase from Escherichia Coli: Reversible Decamer Assembly Controls Enzyme Activity.
Authors: Andrell, J. / Hicks, M.G. / Palmer, T. / Carpenter, E.P. / Iwata, S. / Maher, M.J.
History
DepositionJul 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 12, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Revision 1.3Dec 2, 2015Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIODEGRADATIVE ARGININE DECARBOXYLASE
B: BIODEGRADATIVE ARGININE DECARBOXYLASE
C: BIODEGRADATIVE ARGININE DECARBOXYLASE
D: BIODEGRADATIVE ARGININE DECARBOXYLASE
E: BIODEGRADATIVE ARGININE DECARBOXYLASE
F: BIODEGRADATIVE ARGININE DECARBOXYLASE
G: BIODEGRADATIVE ARGININE DECARBOXYLASE
H: BIODEGRADATIVE ARGININE DECARBOXYLASE
I: BIODEGRADATIVE ARGININE DECARBOXYLASE
J: BIODEGRADATIVE ARGININE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)847,59220
Polymers845,12110
Non-polymers2,47110
Water46,3352572
1
A: BIODEGRADATIVE ARGININE DECARBOXYLASE
B: BIODEGRADATIVE ARGININE DECARBOXYLASE
C: BIODEGRADATIVE ARGININE DECARBOXYLASE
D: BIODEGRADATIVE ARGININE DECARBOXYLASE
E: BIODEGRADATIVE ARGININE DECARBOXYLASE
hetero molecules

A: BIODEGRADATIVE ARGININE DECARBOXYLASE
B: BIODEGRADATIVE ARGININE DECARBOXYLASE
C: BIODEGRADATIVE ARGININE DECARBOXYLASE
D: BIODEGRADATIVE ARGININE DECARBOXYLASE
E: BIODEGRADATIVE ARGININE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)847,59220
Polymers845,12110
Non-polymers2,47110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area77420 Å2
ΔGint-337.1 kcal/mol
Surface area241230 Å2
MethodPISA
2
F: BIODEGRADATIVE ARGININE DECARBOXYLASE
G: BIODEGRADATIVE ARGININE DECARBOXYLASE
H: BIODEGRADATIVE ARGININE DECARBOXYLASE
I: BIODEGRADATIVE ARGININE DECARBOXYLASE
J: BIODEGRADATIVE ARGININE DECARBOXYLASE
hetero molecules

F: BIODEGRADATIVE ARGININE DECARBOXYLASE
G: BIODEGRADATIVE ARGININE DECARBOXYLASE
H: BIODEGRADATIVE ARGININE DECARBOXYLASE
I: BIODEGRADATIVE ARGININE DECARBOXYLASE
J: BIODEGRADATIVE ARGININE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)847,59220
Polymers845,12110
Non-polymers2,47110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area77860 Å2
ΔGint-342 kcal/mol
Surface area241660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.651, 197.651, 450.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11F-2191-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.366, -0.191, 0.911), (-0.2, 0.94, 0.278), (-0.909, -0.284, 0.306)24.67459, 8.12843, 118.6142
2given(-0.652, -0.513, 0.558), (-0.513, 0.841, 0.174), (-0.559, -0.172, -0.811)140.03667, 42.93422, 130.76035
3given(-0.649, -0.509, -0.565), (-0.509, 0.843, -0.174), (0.565, 0.175, -0.806)186.66284, 57.09647, 19.40119
4given(0.372, -0.198, -0.907), (-0.195, 0.939, -0.285), (0.908, 0.282, 0.31)100.05219, 30.94584, -60.90881
5given(0.191, 0.372, 0.908), (0.372, -0.884, 0.284), (0.908, 0.284, -0.307)-7.40155, 37.0991, -27.25466
6given(-0.827, 0.052, 0.56), (0.056, -0.983, 0.175), (0.559, 0.176, 0.81)107.62558, 72.78818, -39.41396
7given(-0.822, 0.054, -0.566), (0.056, -0.983, -0.176), (-0.566, -0.176, 0.805)154.10448, 87.45607, 72.10784
8given(0.196, 0.366, -0.91), (0.37, -0.887, -0.277), (-0.908, -0.283, -0.309)68.07512, 60.90019, 152.2744
9given(0.823, 0.568, 0.007), (0.568, -0.823, 0.004), (0.008, -1)-32.09483, 29.57395, 90.39024

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Components

#1: Protein
BIODEGRADATIVE ARGININE DECARBOXYLASE / ARGININE DECARBOXYLASE


Mass: 84512.062 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Details: COVELENT BOND BETWEEN COFACTOR PYRIDOXAL 5' PHOSPHATE (PLP) AND RESIDUE LYS386.
Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / References: UniProt: P28629, arginine decarboxylase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2572 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.99 Å3/Da / Density % sol: 58.88 % / Description: NONE
Crystal growpH: 6.5
Details: 100 MM MES PH 6.5, 13% PEG 8000 AND 400 MM SODIUM ACETATE

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
3771
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-410.93
SYNCHROTRONESRF ID14-320.93
SYNCHROTRONESRF ID14-430.93
Detector
TypeIDDetectorDateDetails
ADSC CCD1CCDDec 7, 2006MIRRORS
ADSC CCD2CCD
ADSC CCD3CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE SILICON (111) MONOCHROMATORSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 385411 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.778 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.229 19417 5 %RANDOM
Rwork0.177 ---
obs0.179 366476 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.37 Å20 Å2
2--0.75 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59390 0 150 2572 62112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02261898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.94284171
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15657540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40624.1253074
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1891510034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.11115384
X-RAY DIFFRACTIONr_chiral_restr0.0930.29034
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0248100
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.229052
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.241997
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.23672
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.2912
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.2152
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.691.538749
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.163260962
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.71326641
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6974.523209
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 1426 -
Rwork0.254 27111 -
obs--99.99 %
Refinement TLS params.

S31: 0 Å ° / 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 °)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)
10.23460.0558-0.09830.2556-0.03280.2132-0.0050.0671-0.0066-0.0799-0.0008-0.0369-0.00240.00580.0890.0091-0.01530.0972-0.00130.1018150.9338-3.594122.2759
20.1479-0.01010.07870.2261-0.03290.32870.00570.038-0.0202-0.0567-0.00260.06430.0436-0.00320.09340.00530.01610.1001-0.0040.1095101.0991-19.2273-10.8025
30.347-0.00510.00910.2107-0.03620.12670.0021-0.0452-0.04410.05020.00240.06520.0222-0.00450.11660.0003-0.00490.0943-0.01140.088555.9888-33.577528.7267
40.1845-0.0815-0.07830.21590.01640.3264-0.0127-0.0690.00460.07990.0056-0.0270.00730.0070.0868-0.0144-0.00240.08520.00280.113177.8472-26.675585.8728
50.25650.03220.08530.27370.09950.21720.00380.0020.0148-0.00010.0058-0.086-0.0202-0.00970.10630.00530.00670.09190.01570.0828136.4995-8.205581.9046
60.1697-0.0503-0.04180.1927-0.07150.3284-0.0029-0.0425-0.02120.05350.00650.06480.0046-0.00360.0975-0.007-0.01060.087-0.01330.105640.432102.7908101.7942
70.30290.07630.00380.2641-0.03550.14030.00170.0444-0.0012-0.05150.00190.07870.0216-0.00360.10540.01160.00990.0957-0.00670.0855-4.858288.672262.4028
80.13520.00250.05360.26950.07140.3339-0.00280.06360.0122-0.0847-0.003-0.0254-0.02550.00590.07610.00440.00030.09790.00440.11417.089895.54385.1917
90.2855-0.0129-0.12010.24060.01710.20420.0104-0.0040.0364-0.0017-0.0006-0.079-0.0396-0.00970.11050.0045-0.01380.09690.00670.086675.9231113.76379.1458
100.283-0.040.1010.2040.0320.212-0.015-0.0710.0260.0140.017-0.027-0.0120.0760.098-0.0090.0140.0860.0080.10190.2728118.30169.0021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 755
2X-RAY DIFFRACTION2B1 - 755
3X-RAY DIFFRACTION3C1 - 755
4X-RAY DIFFRACTION4D1 - 755
5X-RAY DIFFRACTION5E1 - 755
6X-RAY DIFFRACTION6F1 - 755
7X-RAY DIFFRACTION7G1 - 755
8X-RAY DIFFRACTION8H1 - 755
9X-RAY DIFFRACTION9I1 - 755
10X-RAY DIFFRACTION10J1 - 755

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