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- PDB-2jer: Agmatine deiminase of Enterococcus faecalis catalyzing its reaction. -

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Basic information

Entry
Database: PDB / ID: 2jer
TitleAgmatine deiminase of Enterococcus faecalis catalyzing its reaction.
ComponentsAGMATINE DEIMINASE
KeywordsHYDROLASE / AGMATINE DEIMINASE / TETRAMER / AGDI / 5- FOLD PSEUDOSYMMETRIC STRUCTURE / AGMATINE DEGRADATION PATHWAY / COVALENT AMIDINO ADDUCT / AGMATINE IMINOHYDROLASE
Function / homologyPeptidyl-arginine deiminase, Porphyromonas-type / Agmatine deiminase / Porphyromonas-type peptidyl-arginine deiminase / agmatine deiminase / agmatine deiminase activity / putrescine biosynthetic process / protein-arginine deiminase activity / Putative agmatine deiminase
Function and homology information
Specimen sourceENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.65 Å resolution
AuthorsTavarez, S. / Llacer, J.L. / Rubio, V.
CitationJournal: J.Bacteriol. / Year: 2007
Title: The Gene Cluster for Agmatine Catabolism of Enterococcus Faecalis: Study of Recombinant Putrescine Transcarbamylase and Agmatine Deiminase and a Snapshot of Agmatine Deiminase Catalyzing its Reaction.
Authors: Llacer, J.L. / Polo, L.M. / Tavarez, S. / Alarcon, B. / Hilario, R. / Rubio, V.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 19, 2007 / Release: Jan 30, 2007
RevisionDateData content typeGroupProviderType
1.0Jan 30, 2007Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGMATINE DEIMINASE
B: AGMATINE DEIMINASE
C: AGMATINE DEIMINASE
D: AGMATINE DEIMINASE
E: AGMATINE DEIMINASE
F: AGMATINE DEIMINASE
G: AGMATINE DEIMINASE
H: AGMATINE DEIMINASE


Theoretical massNumber of molelcules
Total (without water)351,6828
Polyers351,6828
Non-polymers00
Water39,1652174
1
A: AGMATINE DEIMINASE
B: AGMATINE DEIMINASE
E: AGMATINE DEIMINASE
F: AGMATINE DEIMINASE


Theoretical massNumber of molelcules
Total (without water)175,8414
Polyers175,8414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: AGMATINE DEIMINASE
D: AGMATINE DEIMINASE
G: AGMATINE DEIMINASE
H: AGMATINE DEIMINASE


Theoretical massNumber of molelcules
Total (without water)175,8414
Polyers175,8414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)107.727, 130.165, 126.726
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide
AGMATINE DEIMINASE / / AGMATINE IMINOHYDROLASE


Mass: 43960.301 Da / Num. of mol.: 8
Details: CARBON ATOM OF THE GUANIDINIUM GROUP OF AGMATINE COVALENTLY LINKED WITH THE THIOL GROUP OF CYS357
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: SD10 / Plasmid name: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q837U5, agmatine deiminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2174 / Formula: H2O / Water
Sequence detailsTHE HIS325 OF UNIPROT DATABASE IS AN ARGININE IN THIS E. FAECALIS STRAIN. THE CRYSTAL STRUCTURE ...THE HIS325 OF UNIPROT DATABASE IS AN ARGININE IN THIS E. FAECALIS STRAIN. THE CRYSTAL STRUCTURE INCLUDE THE 24- AMINO ACID C-TERMINAL EXTENSION VGGKQNSSSVDKLAAALEHHHHHH

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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: 2.5 / Density percent sol: 51 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.5M SODIUM CHLORIDE, 1.6M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 5MM AGMATINE

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9765
DetectorType: MARRESEARCH / Detector: CCD / Collection date: Nov 17, 2005
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionD resolution high: 1.65 Å / D resolution low: 45.36 Å / Number obs: 417377 / Observed criterion sigma I: 2 / Rmerge I obs: 0.08 / NetI over sigmaI: 8.4 / Redundancy: 3.7 % / Percent possible obs: 1
Reflection shellRmerge I obs: 0.44 / Highest resolution: 1.65 Å / Lowest resolution: 1.74 Å / MeanI over sigI obs: 2 / Redundancy: 3.5 % / Percent possible all: 1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EWO
Correlation coeff Fo to Fc: 0.96 / Correlation coeff Fo to Fc free: 0.947 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. / Overall SU B: 3.364 / Overall SU ML: 0.052 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.109 / Overall ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 5.48 Å2 / Aniso B11: 0.76 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0.44 Å2 / Aniso B22: -0.62 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.08 Å2
Least-squares processR factor R free: 0.192 / R factor R work: 0.167 / R factor obs: 0.168 / Highest resolution: 1.65 Å / Lowest resolution: 5 Å / Number reflection R free: 20970 / Number reflection obs: 396242 / Percent reflection R free: 5 / Percent reflection obs: 1
Refine hist #LASTHighest resolution: 1.65 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 23234 / Nucleic acid: 0 / Ligand: 0 / Solvent: 2174 / Total: 25408
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02223752
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.94632208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4735.0002911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83925.4311217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38915.0003935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.17315.000119
X-RAY DIFFRACTIONr_chiral_restr0.1540.2003442
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02018451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.20012051
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.20016425
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2001916
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.20050
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.20014
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8551.50014925
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2362.00023579
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0453.00010059
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1974.5008629
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
Refine LS restraints ncs

Refine ID: X-RAY DIFFRACTION

Dom IDAuth asym IDEns IDNumberTypeRms dev positionWeight position
1A11874tight positional0.060.05
2B11874tight positional0.050.05
3C11874tight positional0.060.05
4D11874tight positional0.060.05
5E11874tight positional0.040.05
6F11874tight positional0.050.05
7G11874tight positional0.040.05
8H11874tight positional0.040.05
1A1793medium positional0.450.50
2B1793medium positional0.550.50
3C1793medium positional0.480.50
4D1793medium positional0.510.50
5E1793medium positional0.530.50
6F1793medium positional0.510.50
7G1793medium positional0.450.50
8H1793medium positional0.420.50
1A1103loose positional0.545.00
2B1103loose positional0.605.00
3C1103loose positional0.645.00
4D1103loose positional1.335.00
5E1103loose positional0.465.00
6F1103loose positional0.405.00
7G1103loose positional0.545.00
8H1103loose positional0.505.00
1E2100loose positional0.265.00
2G2100loose positional0.445.00
3H2100loose positional0.475.00
1A393loose positional0.235.00
2B393loose positional0.245.00
3C393loose positional0.235.00
4D393loose positional0.445.00
5F393loose positional0.165.00
1A11874tight thermal0.170.50
2B11874tight thermal0.160.50
3C11874tight thermal0.160.50
4D11874tight thermal0.150.50
5E11874tight thermal0.140.50
6F11874tight thermal0.140.50
7G11874tight thermal0.120.50
8H11874tight thermal0.130.50
1A1793medium thermal0.862.00
2B1793medium thermal0.882.00
3C1793medium thermal0.822.00
4D1793medium thermal0.862.00
5E1793medium thermal0.792.00
6F1793medium thermal0.732.00
7G1793medium thermal0.642.00
8H1793medium thermal0.652.00
1A1103loose thermal1.7810.00
2B1103loose thermal1.9310.00
3C1103loose thermal2.0310.00
4D1103loose thermal1.9210.00
5E1103loose thermal2.2610.00
6F1103loose thermal1.5710.00
7G1103loose thermal1.4810.00
8H1103loose thermal1.4910.00
1E2100loose thermal2.2910.00
2G2100loose thermal1.6310.00
3H2100loose thermal1.8310.00
1A393loose thermal1.1710.00
2B393loose thermal1.6410.00
3C393loose thermal1.1910.00
4D393loose thermal3.3010.00
5F393loose thermal1.4510.00
Refine LS shellHighest resolution: 1.65 Å / R factor R free: 0.248 / R factor R work: 0.202 / Lowest resolution: 1.69 Å / Number reflection R free: 1485 / Number reflection R work: 29288 / Total number of bins used: 20 / Percent reflection obs: 99.88
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.5808-0.1871-0.15620.9274-0.04530.6720-0.01520.0433-0.0018-0.05590.03640.05240.0226-0.0756-0.0211-0.1503-0.0115-0.0161-0.11380.0023-0.123621.6370-10.126060.2780
20.72470.2198-0.12970.9761-0.11230.7947-0.04490.05810.02480.00960.05910.07060.0120-0.0936-0.0142-0.1375-0.0196-0.0084-0.1128-0.0112-0.126220.9430-33.724057.9860
30.66470.0892-0.00011.00540.02460.8344-0.03440.03550.00250.01750.02920.01980.03660.00350.0052-0.13780.0245-0.0059-0.11950.0071-0.13900.0140-41.549098.2390
40.57020.0029-0.13641.2173-0.15450.7566-0.00230.02460.01530.05580.0498-0.0139-0.04730.0006-0.0476-0.12390.0319-0.0039-0.11750.0070-0.1265-2.2600-18.109097.6400
50.7982-0.32510.00301.0475-0.06460.4786-0.0481-0.02550.04120.04180.0519-0.2032-0.00290.0687-0.0038-0.13790.0070-0.0358-0.0954-0.0226-0.075354.5130-28.535075.1400
60.66600.0862-0.04200.8627-0.16100.6140-0.0311-0.01260.0021-0.03320.0195-0.2174-0.02580.05190.0115-0.1343-0.02250.0162-0.1037-0.0190-0.041557.8320-18.707053.9060
70.62570.19440.03051.1425-0.48810.75180.0677-0.06170.05450.42720.05630.2137-0.1250-0.0622-0.12410.08770.05490.1221-0.07030.0241-0.0565-20.1760-36.2510130.0340
80.90820.3128-0.20331.1689-0.30700.81080.1255-0.09890.07280.5768-0.03940.0998-0.15750.0203-0.08600.20780.01020.0214-0.0764-0.0139-0.12830.8310-26.4500135.4780
90.7049-0.26780.03310.9072-0.29990.9970-0.0433-0.05110.15440.07850.0454-0.0565-0.1869-0.0156-0.0020-0.10660.0001-0.0263-0.1020-0.0037-0.071822.02008.258065.0310
100.96590.5374-0.25000.8968-0.18390.8160-0.12330.1599-0.2230-0.08630.0708-0.06240.1789-0.02430.0526-0.0646-0.03340.0188-0.0840-0.0395-0.055321.0180-52.092053.2750
110.8449-0.03800.06430.80280.05530.9013-0.0126-0.0165-0.18450.04840.0080-0.02390.30550.07720.0045-0.01010.04110.0015-0.09060.0093-0.08244.9310-59.838098.7450
120.81280.1566-0.06661.1005-0.24150.79780.0516-0.01900.19060.15300.04940.1010-0.2438-0.0968-0.1011-0.02000.05560.0443-0.08890.0100-0.0554-7.56900.133098.3460
130.8176-0.5124-0.00271.43770.04270.5165-0.1978-0.3311-0.01590.38750.1940-0.08720.05830.03840.0037-0.01310.0847-0.05380.0245-0.0096-0.062851.2600-33.449093.2290
140.94770.3249-0.25241.24420.02120.4689-0.07530.19070.0080-0.32160.0822-0.2327-0.04270.0096-0.0069-0.0302-0.04730.0726-0.0492-0.0078-0.003660.9970-13.683035.9220
150.49670.3680-0.31251.8880-0.72851.15370.07230.08940.10350.33640.19390.6444-0.0782-0.4025-0.26620.04730.06690.18230.07560.10760.1695-37.7920-41.5630125.4900
160.47570.24260.27051.98680.13241.03090.1646-0.09890.02760.6419-0.0750-0.2858-0.15530.2773-0.08970.3051-0.0579-0.10630.0326-0.0116-0.062918.4910-21.1960139.9670
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1A1A1511
2A360A3671
3B1B1512
4B360B3662
5C1C1513
6C360C3683
7D1D1514
8D360D3734
9E1E1515
10E360E3685
11F1F1516
12F360F3666
13G1G1517
14G360G3677
15H1H1518
16H360H3668
17A160A3549
18B160B35410
19C160C35411
20D160D35412
21E160E35413
22F160F35414
23G160G35415
24H160H35416

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