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- PDB-6g1f: Crystal structure of D-phenylglycine aninotransferase (D-PhgAT) f... -

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Basic information

Entry
Database: PDB / ID: 6g1f
TitleCrystal structure of D-phenylglycine aninotransferase (D-PhgAT) from Pseudomonas stutzeri with PLP internal aldimine
ComponentsD-phenylglycine aminotransferase
KeywordsTRANSFERASE / aminotransferase / PLP / phenylglycine
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å
AuthorsSerpico, A. / Marles-Wright, J. / Campopiano, D.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
IBioIC United Kingdom
CitationJournal: Catalysis Science And Technology / Year: 2020
Title: D-Phenylglycine aminotransferase (D-PhgAT) – substrate scope and structural insights of a stereo-inverting biocatalyst used in the preparation of aromatic amino acids
Authors: Serpico, A. / De Cesare, S. / Marles-Wright, J. / Kalim Akhtar, M. / Loake, G.J. / Campopiano, D.J.
History
DepositionMar 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-phenylglycine aminotransferase
B: D-phenylglycine aminotransferase
C: D-phenylglycine aminotransferase
D: D-phenylglycine aminotransferase
E: D-phenylglycine aminotransferase
F: D-phenylglycine aminotransferase


Theoretical massNumber of molelcules
Total (without water)303,2216
Polymers303,2216
Non-polymers00
Water7,368409
1
A: D-phenylglycine aminotransferase
C: D-phenylglycine aminotransferase


Theoretical massNumber of molelcules
Total (without water)101,0742
Polymers101,0742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-42 kcal/mol
Surface area28790 Å2
MethodPISA
2
B: D-phenylglycine aminotransferase
D: D-phenylglycine aminotransferase


Theoretical massNumber of molelcules
Total (without water)101,0742
Polymers101,0742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-43 kcal/mol
Surface area28670 Å2
MethodPISA
3
E: D-phenylglycine aminotransferase
F: D-phenylglycine aminotransferase


Theoretical massNumber of molelcules
Total (without water)101,0742
Polymers101,0742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-42 kcal/mol
Surface area29170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)329.280, 83.900, 133.420
Angle α, β, γ (deg.)90.00, 111.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
D-phenylglycine aminotransferase


Mass: 50536.812 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Internal PLP aldimine at residue 280 / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: dpgA / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6VY99
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: Yellow crystals, indicating the presence of PLP, were produced by adding 1 uL of 9.1 mg/ml D-PhgAT in 0.1 M CAPS, pH 9.5, 150 mM NaCl, 50 uM PLP to 1 yL of 0.1 M Tris-HCl, pH 7.5, 0.2 M ...Details: Yellow crystals, indicating the presence of PLP, were produced by adding 1 uL of 9.1 mg/ml D-PhgAT in 0.1 M CAPS, pH 9.5, 150 mM NaCl, 50 uM PLP to 1 yL of 0.1 M Tris-HCl, pH 7.5, 0.2 M MgCl2, 10 % (w/v) polyethylene glycol 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2017
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.248→49.47 Å / Num. obs: 160811 / % possible obs: 99.76 % / Redundancy: 6.8 % / Biso Wilson estimate: 49.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.046 / Rrim(I) all: 0.091 / Net I/σ(I): 12.1
Reflection shellResolution: 2.248→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7687 / CC1/2: 0.562 / Rpim(I) all: 0.602 / Rrim(I) all: 0.895 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CY8
Resolution: 2.248→49.466 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 8144 5.07 %
Rwork0.1828 --
obs0.1843 160770 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.248→49.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20233 0 0 409 20642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320690
X-RAY DIFFRACTIONf_angle_d0.54328053
X-RAY DIFFRACTIONf_dihedral_angle_d10.21112100
X-RAY DIFFRACTIONf_chiral_restr0.0393079
X-RAY DIFFRACTIONf_plane_restr0.0033699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2482-2.27370.32532460.31474861X-RAY DIFFRACTION95
2.2737-2.30050.31272800.28345037X-RAY DIFFRACTION100
2.3005-2.32850.30142560.26765117X-RAY DIFFRACTION100
2.3285-2.3580.28992610.25565016X-RAY DIFFRACTION100
2.358-2.3890.28262690.25415114X-RAY DIFFRACTION100
2.389-2.42180.27792380.24365040X-RAY DIFFRACTION100
2.4218-2.45640.27562650.22435115X-RAY DIFFRACTION100
2.4564-2.4930.25372480.21435082X-RAY DIFFRACTION100
2.493-2.5320.23552710.21195062X-RAY DIFFRACTION100
2.532-2.57350.25172700.20535065X-RAY DIFFRACTION100
2.5735-2.61790.23422900.20165076X-RAY DIFFRACTION100
2.6179-2.66550.23562690.19865031X-RAY DIFFRACTION100
2.6655-2.71670.22632790.19745100X-RAY DIFFRACTION100
2.7167-2.77220.2262790.20365064X-RAY DIFFRACTION100
2.7722-2.83250.21942630.20575065X-RAY DIFFRACTION100
2.8325-2.89830.23032750.20185110X-RAY DIFFRACTION100
2.8983-2.97080.25542450.20155098X-RAY DIFFRACTION100
2.9708-3.05110.24722730.20885068X-RAY DIFFRACTION100
3.0511-3.14090.24492790.20585109X-RAY DIFFRACTION100
3.1409-3.24230.24122900.2155079X-RAY DIFFRACTION100
3.2423-3.35810.24122860.21175078X-RAY DIFFRACTION100
3.3581-3.49250.24952590.1985115X-RAY DIFFRACTION100
3.4925-3.65140.21422780.18025095X-RAY DIFFRACTION100
3.6514-3.84390.20242710.16855105X-RAY DIFFRACTION100
3.8439-4.08460.1712940.15485048X-RAY DIFFRACTION100
4.0846-4.39980.1763080.14935134X-RAY DIFFRACTION100
4.3998-4.84220.16463020.14285093X-RAY DIFFRACTION100
4.8422-5.54210.18892520.15565166X-RAY DIFFRACTION100
5.5421-6.97930.21382700.1785201X-RAY DIFFRACTION100
6.9793-49.47770.16742780.15745282X-RAY DIFFRACTION100
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)
10.98990.286-0.8180.260.20091.4476-0.02930.4843-0.03020.15960.09520.07140.2769-0.28470.00010.39970.02420.02190.56830.05630.469649.0122-1.438334.2132
21.8384-0.4362-0.21891.6451-0.35420.86510.0314-0.0471-0.2617-0.05930.04310.15310.1032-0.0515-00.4684-0.0343-0.01990.39760.00830.462176.1692-13.573144.3338
30.9984-0.5315-0.66230.85120.04770.56740.0569-0.612-0.40670.2024-0.1441-0.0550.08880.09030.00010.4669-0.07690.0310.4580.04540.441854.0209-11.555358.9569
41.0631-0.5964-0.66171.17790.21140.50270.04330.09510.28740.1518-0.01050.1483-0.0482-0.01700.4601-0.03210.03780.5-0.03080.522846.9031-4.202350.7515
50.6554-0.2808-0.20741.33240.76370.385-0.0313-0.0682-0.05320.06-0.010.055-0.0362-0.073200.4271-0.00570.01190.4-0.0010.513389.113227.199661.0169
61.25660.67-0.66491.230.55311.1567-0.0410.21240.1494-0.12790.2157-0.136-0.2635-0.124800.42580.0406-0.02110.5029-0.03870.5376115.089937.635366.4852
70.38630.76740.06851.5733-0.09781.1421-0.02580.487-0.0518-0.56580.0707-0.0718-0.1791-0.1505-00.7089-0.08920.12660.7177-0.12540.7203121.815442.027445.3903
81.34110.5663-0.25521.6164-0.14271.2526-0.05770.01530.02990.0230.2148-0.408-0.02370.24920.00010.36160.0313-0.02830.4749-0.09320.5053121.574334.751264.4469
90.90390.4736-0.25570.7560.49110.9806-0.13960.1866-0.2301-0.02330.3169-0.3244-0.01480.488800.41140.0190.03940.4064-0.09550.4914111.083714.827250.231
100.75450.1232-0.55190.54650.62431.2188-0.169-0.3327-0.21160.2279-0.0408-0.13320.3282-0.0288-0.00140.3903-0.0161-0.00440.2706-0.03210.507698.562515.006755.1639
111.37310.728-0.79440.3109-0.00822.2558-0.06940.14240.0168-0.05680.104-0.15940.0460.3549-00.4281-0.05370.02820.408-0.01190.421295.66443.594931.3838
122.05450.9766-0.40181.74650.56111.3035-0.10420.4373-0.10720.04550.2253-0.14510.1937-0.0452-0.00010.5701-0.0521-0.03170.61710.0060.487371.1309-8.483723.4754
132.09060.1642-0.52172.65980.28161.5365-0.11770.5037-0.2862-0.16140.1523-0.00970.226-0.2030.00490.4754-0.1177-0.01530.6047-0.11270.410371.8288-15.470516.6639
141.53330.2502-0.99680.4565-0.00490.56-0.34860.99-0.5727-0.22170.25210.00750.1269-0.0967-0.01820.5665-0.11530.06530.7728-0.11950.407692.3427-4.67095.4159
150.33570.4331-0.12160.88310.340.91360.04280.62070.2173-0.31160.14620.005-0.07390.0296-0.00010.57-0.07010.05920.71210.04890.533597.6293.374214.9058
160.979-0.54690.03131.1910.79960.66880.0286-0.27690.11590.29280.1408-0.1986-0.2381-0.04090.00010.58440.0645-0.14820.5197-0.12450.4532120.451648.767489.0593
170.33310.22270.47691.2995-0.28890.694-0.0673-0.02770.0240.01710.04310.04970.07380.030900.41070.06140.01030.4011-0.01650.425596.980544.037470.6647
180.34130.2194-0.28430.5992-0.10840.234-0.0662-0.0491-0.01550.25980.1005-0.935-0.07260.8102-0.00040.7313-0.0118-0.08960.7849-0.01160.8991111.378760.377161.2004
191.54280.24060.06861.5666-0.40961.9623-0.0629-0.06950.26530.07260.0613-0.003-0.24630.126-00.39820.0184-0.01660.3131-0.02850.419399.565457.401763.6343
201.11810.1170.27030.5515-0.21380.2595-0.233-0.53010.39590.09090.03560.1597-0.4272-0.2334-0.04470.6660.0746-0.04570.4884-0.19220.5272105.002870.881285.1228
210.31480.12150.48041.3685-0.09670.90420.0355-0.37140.09280.59110.119-0.0036-0.1132-0.31530.04910.59160.1041-0.08860.588-0.20390.4091112.01662.442292.9339
220.5160.55680.52261.52041.00640.6986-0.04820.2844-0.2270.13880.073-0.59870.08620.36480.00020.64280.0629-0.07760.720.04180.9252154.153413.139222.5869
231.13620.4710.36861.94280.43821.91-0.24950.39520.0103-0.3957-0.0643-0.1503-0.26670.071500.6327-0.0655-0.00920.85570.03290.6574132.224521.99583.0211
241.07410.88090.09981.25870.53850.4316-0.20890.2765-0.2366-0.2775-0.18060.10460.2393-0.1506-0.03350.5386-0.0413-0.01470.7239-0.06970.5596125.517116.76785.5788
250.67580.52260.61980.82970.16070.5715-0.3027-0.20050.3669-0.011-0.15240.2879-0.2797-0.1965-0.08490.530.0052-0.13110.47720.03640.5488139.325535.907723.1977
260.69140.8673-0.00640.98540.1280.85540.2107-0.1404-0.35570.3609-0.0873-0.18660.07610.07100.5133-0.0086-0.11220.56670.01950.5476147.132426.536829.1101
270.9285-0.0187-0.08991.34130.74330.5483-0.17680.5449-0.2083-0.19080.0058-0.14640.3468-0.2751-0.00120.801-0.24410.21080.9729-0.2330.7588117.4605-5.82810.3959
281.69240.2891-0.33241.07240.83951.8098-0.14920.48780.02410.0293-0.0344-0.26660.1680.172100.6796-0.00250.12410.83320.00060.9629145.3142.7823.509
290.14560.2537-0.19640.449-0.39370.26880.04920.02670.1765-0.5586-0.5370.7285-0.6789-0.5185-0.00011.1086-0.09450.12971.3749-0.0261.1719139.351310.0306-18.7471
300.2364-0.17510.13571.32540.98061.16950.03230.5479-0.0704-0.3628-0.0464-0.25180.14120.3655-0.00010.74540.02850.2511.12750.01750.9399151.18390.3273-9.8263
310.54190.6639-0.11310.9839-0.33330.86060.01170.208-0.1631-0.1525-0.1137-0.65930.19320.3737-0.35640.73670.08050.22440.7798-0.09080.8834143.8024-7.40041.6402
320.77270.81340.30511.15460.08940.4509-0.10620.4137-0.4893-0.2369-0.2287-0.12010.65670.2746-0.09410.8688-0.09790.26840.8897-0.27790.7646129.3966-17.0881-11.8738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 325 )
3X-RAY DIFFRACTION3chain 'A' and (resid 326 through 386 )
4X-RAY DIFFRACTION4chain 'A' and (resid 387 through 443 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 60 )
6X-RAY DIFFRACTION6chain 'B' and (resid 61 through 165 )
7X-RAY DIFFRACTION7chain 'B' and (resid 166 through 208 )
8X-RAY DIFFRACTION8chain 'B' and (resid 209 through 325 )
9X-RAY DIFFRACTION9chain 'B' and (resid 326 through 386 )
10X-RAY DIFFRACTION10chain 'B' and (resid 387 through 441 )
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 60 )
12X-RAY DIFFRACTION12chain 'C' and (resid 61 through 165 )
13X-RAY DIFFRACTION13chain 'C' and (resid 166 through 325 )
14X-RAY DIFFRACTION14chain 'C' and (resid 326 through 386 )
15X-RAY DIFFRACTION15chain 'C' and (resid 387 through 441 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 60 )
17X-RAY DIFFRACTION17chain 'D' and (resid 61 through 137 )
18X-RAY DIFFRACTION18chain 'D' and (resid 138 through 165 )
19X-RAY DIFFRACTION19chain 'D' and (resid 166 through 325 )
20X-RAY DIFFRACTION20chain 'D' and (resid 326 through 386 )
21X-RAY DIFFRACTION21chain 'D' and (resid 387 through 441 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 60 )
23X-RAY DIFFRACTION23chain 'E' and (resid 61 through 233 )
24X-RAY DIFFRACTION24chain 'E' and (resid 234 through 325 )
25X-RAY DIFFRACTION25chain 'E' and (resid 326 through 386 )
26X-RAY DIFFRACTION26chain 'E' and (resid 387 through 441 )
27X-RAY DIFFRACTION27chain 'F' and (resid 1 through 60 )
28X-RAY DIFFRACTION28chain 'F' and (resid 61 through 153 )
29X-RAY DIFFRACTION29chain 'F' and (resid 154 through 187 )
30X-RAY DIFFRACTION30chain 'F' and (resid 188 through 290 )
31X-RAY DIFFRACTION31chain 'F' and (resid 291 through 348 )
32X-RAY DIFFRACTION32chain 'F' and (resid 349 through 438 )

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