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

ID or keywords:

Entry

Database: PDB / ID: 2vyc

Title

Crystal Structure of Acid Induced Arginine Decarboxylase from E. coli

Components

BIODEGRADATIVE ARGININE DECARBOXYLASE

Keywords

LYASE / 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

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 2.4 Å

Authors

Andrell, J. / Hicks, M.G. / Palmer, T. / Carpenter, E.P. / Iwata, S. / Maher, M.J.

Citation

Journal: 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

Deposition	Jul 22, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 31, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 12, 2011	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Revision 1.3	Dec 2, 2015	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2vyc.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb2vyc.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	2vyc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2vyc_validation.pdf.gz	522.2 KB	Display	wwPDB validaton report
Full document	2vyc_full_validation.pdf.gz	605.3 KB	Display
Data in XML	2vyc_validation.xml.gz	273.5 KB	Display
Data in CIF	2vyc_validation.cif.gz	389 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vy/2vyc ftp://data.pdbj.org/pub/pdb/validation_reports/vy/2vyc	HTTPS FTP

-
Related structure data

Similar structure data	5xx1-d 6q6i-1 3n75-1 10849 6y3x-1 6yn5-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

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

848 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
848 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
848 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	172
Space group name H-M	P6₄

Components on special symmetry positions

ID	Model	Components
1	1	F-2191- HOH

Noncrystallographic symmetry (NCS)

NCS oper:

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

#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

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	77	1
2	77	1
3	77	1

Diffraction source

Source	Site	Beamline	ID	Wavelength
SYNCHROTRON	ESRF	ID14-4	1	0.93
SYNCHROTRON	ESRF	ID14-3	2	0.93
SYNCHROTRON	ESRF	ID14-4	3	0.93

Detector

Type	ID	Detector	Date	Details
ADSC CCD	1	CCD	Dec 7, 2006	MIRRORS
ADSC CCD	2	CCD
ADSC CCD	3	CCD

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE SILICON (111) MONOCHROMATOR	SINGLE WAVELENGTH	M	x-ray	1
2		SINGLE WAVELENGTH	M	x-ray	1
3		SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

Wavelength: 0.93 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 385411 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / R_merge(I) obs: 0.15 / Net I/σ(I): 10.7

Reflection shell

Resolution: 2.4→2.49 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MIRAS
Starting model: NONE

Resolution: 2.4→50 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.229	19417	5 %	RANDOM
R_work	0.177	-	-	-
obs	0.179	366476	99.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 23.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.75 Å²	0.37 Å²	0 Å²
2-	-	0.75 Å²	0 Å²
3-	-	-	-1.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	59390	0	150	2572	62112

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	61898
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.345	1.942	84171
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.156	5	7540
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.406	24.125	3074
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.189	15	10034
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.111	15	384
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	9034
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	48100
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	29052
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	41997
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	3672
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.184	0.2	912
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.218	0.2	152
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.69	1.5	38749
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.163	2	60962
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.71	3	26641
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.697	4.5	23209
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.318	1426	-
R_work	0.254	27111	-
obs	-	-	99.99 %

Refinement TLS params.

S31: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.2346	0.0558	-0.0983	0.2556	-0.0328	0.2132	-0.005	0.0671	-0.0066	-0.0799	-0.0008	-0.0369	-0.0024	0.0058	0.089	0.0091	-0.0153	0.0972	-0.0013	0.1018	150.9338	-3.5941	22.2759
2	0.1479	-0.0101	0.0787	0.2261	-0.0329	0.3287	0.0057	0.038	-0.0202	-0.0567	-0.0026	0.0643	0.0436	-0.0032	0.0934	0.0053	0.0161	0.1001	-0.004	0.1095	101.0991	-19.2273	-10.8025
3	0.347	-0.0051	0.0091	0.2107	-0.0362	0.1267	0.0021	-0.0452	-0.0441	0.0502	0.0024	0.0652	0.0222	-0.0045	0.1166	0.0003	-0.0049	0.0943	-0.0114	0.0885	55.9888	-33.5775	28.7267
4	0.1845	-0.0815	-0.0783	0.2159	0.0164	0.3264	-0.0127	-0.069	0.0046	0.0799	0.0056	-0.027	0.0073	0.007	0.0868	-0.0144	-0.0024	0.0852	0.0028	0.1131	77.8472	-26.6755	85.8728
5	0.2565	0.0322	0.0853	0.2737	0.0995	0.2172	0.0038	0.002	0.0148	-0.0001	0.0058	-0.086	-0.0202	-0.0097	0.1063	0.0053	0.0067	0.0919	0.0157	0.0828	136.4995	-8.2055	81.9046
6	0.1697	-0.0503	-0.0418	0.1927	-0.0715	0.3284	-0.0029	-0.0425	-0.0212	0.0535	0.0065	0.0648	0.0046	-0.0036	0.0975	-0.007	-0.0106	0.087	-0.0133	0.1056	40.432	102.7908	101.7942
7	0.3029	0.0763	0.0038	0.2641	-0.0355	0.1403	0.0017	0.0444	-0.0012	-0.0515	0.0019	0.0787	0.0216	-0.0036	0.1054	0.0116	0.0099	0.0957	-0.0067	0.0855	-4.8582	88.6722	62.4028
8	0.1352	0.0025	0.0536	0.2695	0.0714	0.3339	-0.0028	0.0636	0.0122	-0.0847	-0.003	-0.0254	-0.0255	0.0059	0.0761	0.0044	0.0003	0.0979	0.0044	0.114	17.0898	95.5438	5.1917
9	0.2855	-0.0129	-0.1201	0.2406	0.0171	0.2042	0.0104	-0.004	0.0364	-0.0017	-0.0006	-0.079	-0.0396	-0.0097	0.1105	0.0045	-0.0138	0.0969	0.0067	0.0866	75.9231	113.7637	9.1458
10	0.283	-0.04	0.101	0.204	0.032	0.212	-0.015	-0.071	0.026	0.014	0.017	-0.027	-0.012	0.076	0.098	-0.009	0.014	0.086	0.008	0.101	90.2728	118.301	69.0021

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 755
2	X-RAY DIFFRACTION	2	B	1 - 755
3	X-RAY DIFFRACTION	3	C	1 - 755
4	X-RAY DIFFRACTION	4	D	1 - 755
5	X-RAY DIFFRACTION	5	E	1 - 755
6	X-RAY DIFFRACTION	6	F	1 - 755
7	X-RAY DIFFRACTION	7	G	1 - 755
8	X-RAY DIFFRACTION	8	H	1 - 755
9	X-RAY DIFFRACTION	9	I	1 - 755
10	X-RAY DIFFRACTION	10	J	1 - 755

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi