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- PDB-4u1t: The crystal structure of holo CalE6, a methionine gamma lyase fro... -

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Basic information

Entry
Database: PDB / ID: 4u1t
TitleThe crystal structure of holo CalE6, a methionine gamma lyase from Micromonospora echinospora
ComponentsCalE6
KeywordsLYASE
Function / homology
Function and homology information


carbon-sulfur lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / 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 ...Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSong, H.G. / Guo, Z.H.
CitationJournal: Chembiochem / Year: 2015
Title: Identification and Characterization of a Methionine gamma-Lyase in the Calicheamicin Biosynthetic Cluster of Micromonospora echinospora
Authors: Song, H. / Xu, R. / Guo, Z.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 2.0Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 15, 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

Downloads & links

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Assembly

Deposited unit
A: CalE6
B: CalE6
C: CalE6
D: CalE6
E: CalE6
F: CalE6
G: CalE6
H: CalE6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,61916
Polymers335,8518
Non-polymers7698
Water43,9032437
1
A: CalE6
B: CalE6
C: CalE6
D: CalE6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,3108
Polymers167,9254
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18620 Å2
ΔGint-161 kcal/mol
Surface area44610 Å2
MethodPISA
2
E: CalE6
F: CalE6
G: CalE6
H: CalE6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,3108
Polymers167,9254
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18560 Å2
ΔGint-163 kcal/mol
Surface area44770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.170, 146.220, 348.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
CalE6


Mass: 41981.336 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calE6 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KNG3, methionine gamma-lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2437 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, 17% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→47.7 Å / Num. obs: 294248 / % possible obs: 99.9 % / Redundancy: 2 % / Net I/σ(I): 17

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data collection
iMOSFLMdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QI6
Resolution: 2→47.661 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1843 12473 5.02 %
Rwork0.1515 --
obs0.1532 248603 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21897 0 40 2437 24374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822436
X-RAY DIFFRACTIONf_angle_d1.0730641
X-RAY DIFFRACTIONf_dihedral_angle_d12.7368021
X-RAY DIFFRACTIONf_chiral_restr0.0473588
X-RAY DIFFRACTIONf_plane_restr0.0064017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.23534220.17997813X-RAY DIFFRACTION99
2.0227-2.04650.21924090.17177825X-RAY DIFFRACTION100
2.0465-2.07150.21264050.16927757X-RAY DIFFRACTION100
2.0715-2.09770.20534010.1547837X-RAY DIFFRACTION100
2.0977-2.12530.17994010.15117803X-RAY DIFFRACTION100
2.1253-2.15440.19834360.14887850X-RAY DIFFRACTION100
2.1544-2.18520.21424160.1517740X-RAY DIFFRACTION100
2.1852-2.21780.19284280.15777827X-RAY DIFFRACTION99
2.2178-2.25250.26874090.21967859X-RAY DIFFRACTION100
2.2525-2.28940.22083950.19977763X-RAY DIFFRACTION99
2.2894-2.32890.21314400.16167810X-RAY DIFFRACTION99
2.3289-2.37120.1854170.14377822X-RAY DIFFRACTION100
2.3712-2.41680.18943750.14637854X-RAY DIFFRACTION100
2.4168-2.46610.1863620.14767904X-RAY DIFFRACTION100
2.4661-2.51980.19523970.15317890X-RAY DIFFRACTION100
2.5198-2.57840.18774010.14627862X-RAY DIFFRACTION100
2.5784-2.64280.18594090.14147885X-RAY DIFFRACTION100
2.6428-2.71430.18414090.14597864X-RAY DIFFRACTION100
2.7143-2.79420.17724450.1427871X-RAY DIFFRACTION100
2.7942-2.88430.1894160.14677881X-RAY DIFFRACTION100
2.8843-2.98740.18654120.14957881X-RAY DIFFRACTION100
2.9874-3.1070.19234510.14927869X-RAY DIFFRACTION100
3.107-3.24840.17244290.14247892X-RAY DIFFRACTION100
3.2484-3.41960.18264180.14857904X-RAY DIFFRACTION100
3.4196-3.63380.16724440.14987895X-RAY DIFFRACTION100
3.6338-3.91420.16074200.13477974X-RAY DIFFRACTION100
3.9142-4.30790.15514450.13297951X-RAY DIFFRACTION100
4.3079-4.93070.14834150.12967946X-RAY DIFFRACTION100
4.9307-6.210.18634260.16178060X-RAY DIFFRACTION100
6.21-47.67480.18634200.17438041X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.4344-0.30510.17310.274-0.17870.68260.01730.01370.3673-0.0189-0.0058-0.0283-0.1568-0.0419-0.00170.1712-0.01330.01530.08220.00060.1813-30.5076-20.2662-52.8221
20.06660.0384-0.18471.2875-0.08631.04790.03520.6515-0.1272-0.3949-0.0011-0.28460.16570.0995-0.01530.23220.02040.07850.4204-0.04180.1193-24.0517-35.3659-76.0314
30.77020.41060.40350.5996-0.17771.14410.20810.77470.0351-0.4601-0.1429-0.39830.1795-0.0290.53260.32280.0450.24370.46310.0930.2198-11.9483-34.2857-77.9241
40.73590.0328-0.05290.61190.14490.3808-0.02180.26510.1019-0.2189-0.0057-0.122-0.0186-0.02550.02320.1321-0.00920.04360.16550.04310.1082-23.0044-30.1754-65.9224
50.52110.03510.15620.625-0.12690.0473-0.02290.0813-0.0799-0.09180.0069-0.2625-0.00040.040.03330.0857-0.01110.0660.1038-0.00440.159-10.2947-45.8184-57.844
62.1503-0.5974-0.63023.21391.09941.5226-0.05790.0807-0.1753-0.21650.0844-0.03-0.0131-0.0648-0.0280.0827-0.01140.02730.0754-0.01520.1397-15.0547-53.7457-55.9482
71.61890.17090.13370.85830.1290.7841-0.06020.3985-0.0656-0.20030.02280.05150.08540.0464-0.00620.1629-0.0326-0.0130.1689-0.0180.0543-49.6917-40.0316-68.2331
80.67490.01830.14591.31050.18490.549-0.07140.13510.1999-0.22190.00250.2244-0.0642-0.08950.05710.1052-0.0219-0.0520.11570.03150.1503-61.1486-20.5135-59.6216
91.4794-0.22620.01060.75340.32340.8129-0.0247-0.45950.01560.15190.00730.05120.0251-0.01710.00320.1202-0.01510.00960.2218-0.0120.0848-48.9745-29.2855-25.454
101.16010.5595-0.040.8594-0.0310.35420.0025-0.2195-0.04580.0594-0.00240.08420.00520.00740.0150.06270.00620.01410.11190.0090.079-60.1764-41.8498-31.056
112.09510.17920.11260.6237-0.03580.7350.0399-0.1332-0.3574-0.0123-0.01450.09820.1911-0.0834-0.01230.1909-0.01620.0020.10910.01840.1504-31.4899-50.6125-38.5459
120.337-0.18910.56211.0179-0.64852.0285-0.1723-0.7317-0.08140.28330.1601-0.29870.00360.12090.0470.14620.0521-0.04990.4210.0218-0.1352-27.3936-38.9924-17.952
130.20510.0172-0.2660.77540.19840.84620.0394-0.79560.04420.1943-0.0637-0.3132-0.14880.10650.00590.19260.0468-0.10360.5479-0.03520.0695-18.7758-36.8127-14.7222
140.785-0.1587-0.26910.8002-0.04820.5609-0.0014-0.32140.03490.10290.0245-0.12180.06130.0954-0.01760.0707-0.0085-0.01990.1618-0.02330.0759-19.7355-34.3396-30.8875
150.78250.11230.30131.27160.05661.2757-0.0486-0.27630.23290.07640.1889-0.0795-0.25330.20190.08060.1073-0.04060.0070.1865-0.1170.2107-13.4928-19.3215-32.2729
160.2431-0.37130.06871.3908-0.04070.5434-0.0204-0.0078-0.01060.02160.0512-0.40380.05370.163-0.01480.0933-0.0059-0.01320.16120.00030.1837-22.356-41.477-140.535
170.70570.34980.43880.6520.46711.49750.0529-0.20810.30220.8811-0.0424-0.0630.0204-0.14530.15480.37610.0029-0.02950.1386-0.0676-0.0938-35.015-45.482-161.21
180.6974-0.20060.19030.8007-0.00830.494-0.0206-0.27150.15080.4481-0.0115-0.03080.0377-0.03330.03410.2737-0.0203-0.02210.1851-0.0440.0851-35.806-50.978-160.562
191.1517-0.15030.12580.79580.32460.5927-0.0218-0.15010.16140.1326-0.0520.1536-0.04-0.11460.07350.112-0.01590.02270.0856-0.02810.1262-51.26-59.901-146.076
200.3399-0.29150.06771.70790.01220.5766-0.021-0.0598-0.00240.09980.00750.3201-0.071-0.13930.03230.098-0.00730.01770.1623-0.00350.1561-52.144-28.384-140.679
211.34020.264-0.40460.5303-0.29011.7955-0.0193-0.3396-0.18940.7445-0.0433-0.10620.04070.1222-0.05270.33920.0054-0.00830.14970.060.0594-38.87-23.1-160.399
220.76770.0321-0.13180.17220.36980.868-0.1619-0.7114-0.29830.9607-0.0867-0.2350.0740.1565-0.30490.6750.1349-0.25230.14280.4966-0.364-33.449-17.015-168.433
230.5853-0.1278-0.0530.52220.15420.4165-0.0443-0.2719-0.2040.3074-0.01550.0970.0282-0.0120.00350.2018-0.010.04390.16550.06820.1193-40.348-17.758-154.918
240.5563-0.0868-0.01730.47640.12990.3346-0.0302-0.0975-0.24450.1130.0256-0.06170.051-0.01540.02050.0628-0.0167-0.01060.05630.06090.16-26.223-8.427-144.164
252.2661-0.35060.37651.8785-0.5961.81-0.0199-0.3636-0.01370.2666-0.0254-0.1825-0.12440.0420.00990.0885-0.0091-0.0340.10220.01940.1443-17.926-14.011-145.622
260.4354-0.1138-0.15291.6162-0.21670.53130.0175-0.0267-0.02740.03050.0041-0.47950.05740.1094-0.03090.07360.0056-0.01840.16120.00440.1741-22.0125-27.5958-127.9744
270.54240.60460.43231.0006-0.0581.83710.0981-0.0897-0.03650.439-0.1462-0.26810.09790.05040.01770.1944-0.0226-0.02770.1242-0.00450.0548-30.6545-28.6359-111.4002
280.7254-0.02730.01250.94060.01390.64680.0448-0.27110.08730.4343-0.08330.02790.0381-0.03310.02370.2387-0.04160.00230.1817-0.03690.0866-36.3416-20.0853-105.2337
291.0793-0.3195-0.21060.46490.14590.63890.0263-0.06870.08540.1034-0.00680.174-0.0285-0.0688-0.01720.0848-0.00620.03590.0749-0.01560.1433-49.4242-10.892-119.2055
301.5409-0.6135-0.66680.77090.50150.68220.15240.2380.252-0.0216-0.06320.1652-0.3688-0.29860.05180.09960.05730.03590.10310.01310.1807-54.905-8.695-126.029
310.3792-0.28260.08841.69160.48580.41090.0359-0.00960.01570.0155-0.10960.4635-0.0415-0.07080.04550.08850.00930.02660.1514-0.00980.1733-53.5545-43.8608-129.5637
320.66510.5751-0.49240.9782-0.22371.73370.0582-0.06470.00420.5128-0.11220.31060.01580.0145-0.04950.2333-0.01490.03160.12620.00610.0278-46.0744-44.228-112.6075
331.166-0.06550.21940.24720.13641.3111-0.1367-0.3019-0.38210.86570.1236-0.1150.05370.19640.08270.5471-0.0050.00490.18920.14060.0623-39.1375-57.0338-103.3614
340.8006-0.0891-0.00561.06770.16530.53360.015-0.0883-0.110.22490.0087-0.11150.04410.0369-0.01310.1179-0.0008-0.02240.06780.02280.0752-33.2574-57.0554-119.0131
352.8418-0.62540.81411.5516-0.68641.98380.0801-0.09520.03360.2023-0.0666-0.30110.05380.14370.03570.11520.0107-0.05860.0814-0.0030.1831-20.3909-58.701-123.3517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 233 )
5X-RAY DIFFRACTION5chain 'A' and (resid 234 through 314 )
6X-RAY DIFFRACTION6chain 'A' and (resid 315 through 380 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 233 )
8X-RAY DIFFRACTION8chain 'B' and (resid 234 through 379 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 143 )
10X-RAY DIFFRACTION10chain 'C' and (resid 144 through 378 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 65 )
12X-RAY DIFFRACTION12chain 'D' and (resid 66 through 100 )
13X-RAY DIFFRACTION13chain 'D' and (resid 101 through 194 )
14X-RAY DIFFRACTION14chain 'D' and (resid 195 through 284 )
15X-RAY DIFFRACTION15chain 'D' and (resid 285 through 378 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 65 )
17X-RAY DIFFRACTION17chain 'E' and (resid 66 through 100 )
18X-RAY DIFFRACTION18chain 'E' and (resid 101 through 233 )
19X-RAY DIFFRACTION19chain 'E' and (resid 234 through 379 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 65 )
21X-RAY DIFFRACTION21chain 'F' and (resid 66 through 100 )
22X-RAY DIFFRACTION22chain 'F' and (resid 101 through 143 )
23X-RAY DIFFRACTION23chain 'F' and (resid 144 through 233 )
24X-RAY DIFFRACTION24chain 'F' and (resid 234 through 314 )
25X-RAY DIFFRACTION25chain 'F' and (resid 315 through 379 )
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 38 )
27X-RAY DIFFRACTION27chain 'G' and (resid 39 through 100 )
28X-RAY DIFFRACTION28chain 'G' and (resid 101 through 233 )
29X-RAY DIFFRACTION29chain 'G' and (resid 234 through 355 )
30X-RAY DIFFRACTION30chain 'G' and (resid 356 through 378 )
31X-RAY DIFFRACTION31chain 'H' and (resid 1 through 38 )
32X-RAY DIFFRACTION32chain 'H' and (resid 39 through 100 )
33X-RAY DIFFRACTION33chain 'H' and (resid 101 through 194 )
34X-RAY DIFFRACTION34chain 'H' and (resid 195 through 314 )
35X-RAY DIFFRACTION35chain 'H' and (resid 315 through 379 )

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