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- PDB-5uid: The crystal structure of an aminotransferase TlmJ from Streptoall... -

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Basic information

Entry
Database: PDB / ID: 5uid
TitleThe crystal structure of an aminotransferase TlmJ from Streptoalloteichus hindustanus
ComponentsAminotransferase TlmJ
KeywordsTRANSFERASE / Aminotransferase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / TlmJ
Similarity search - Component
Biological speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.18 Å
AuthorsTan, K. / Bigelow, L. / Bearden, J. / Phillips Jr., G.N. / Joachmiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: The crystal structure of an aminotransferase TlmJ from Streptoalloteichus hindustanus.
Authors: Tan, K. / Bigelow, L. / Bearden, J. / Phillips Jr., G.N. / Joachmiak, A.
History
DepositionJan 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase TlmJ
B: Aminotransferase TlmJ
C: Aminotransferase TlmJ
D: Aminotransferase TlmJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,68331
Polymers173,7874
Non-polymers2,89627
Water7,134396
1
A: Aminotransferase TlmJ
B: Aminotransferase TlmJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,48517
Polymers86,8932
Non-polymers1,59215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-201 kcal/mol
Surface area26450 Å2
MethodPISA
2
C: Aminotransferase TlmJ
D: Aminotransferase TlmJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,19714
Polymers86,8932
Non-polymers1,30412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-167 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.601, 198.093, 60.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Aminotransferase TlmJ


Mass: 43446.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus hindustanus (bacteria)
Gene: tlmJ / Plasmid: pMCSG73 / Cell line (production host): BL21 (DE3) pGrow7-K / Production host: Escherichia coli (E. coli) / References: UniProt: A4KUD2
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.8 M Lisium sulfate, 0.1 M Sodium Acetate:HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2012 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.18→40 Å / Num. obs: 84790 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.056 / Χ2: 0.842 / Net I/σ(I): 11.8
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4061 / CC1/2: 0.83 / Rpim(I) all: 0.293 / Χ2: 0.539 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.18→34.9 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.73
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 4182 5.01 %random
Rwork0.1898 ---
obs0.1919 83532 94.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.18→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11101 0 149 397 11647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211486
X-RAY DIFFRACTIONf_angle_d0.4915634
X-RAY DIFFRACTIONf_dihedral_angle_d13.6076728
X-RAY DIFFRACTIONf_chiral_restr0.041717
X-RAY DIFFRACTIONf_plane_restr0.0032032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.20480.28391160.23522386X-RAY DIFFRACTION86
2.2048-2.23070.31421230.22342435X-RAY DIFFRACTION88
2.2307-2.25790.25061340.22292472X-RAY DIFFRACTION89
2.2579-2.28650.25321250.21242453X-RAY DIFFRACTION89
2.2865-2.31660.24891440.22162508X-RAY DIFFRACTION90
2.3166-2.34830.29771530.22572486X-RAY DIFFRACTION91
2.3483-2.38180.28961410.21982512X-RAY DIFFRACTION91
2.3818-2.41740.2981370.22452582X-RAY DIFFRACTION92
2.4174-2.45510.25821390.22332514X-RAY DIFFRACTION92
2.4551-2.49540.2911420.22382583X-RAY DIFFRACTION93
2.4954-2.53840.28451240.22462600X-RAY DIFFRACTION93
2.5384-2.58450.28351370.21842563X-RAY DIFFRACTION93
2.5845-2.63420.28831690.22252612X-RAY DIFFRACTION94
2.6342-2.6880.29321390.22322523X-RAY DIFFRACTION93
2.688-2.74640.25591360.22862632X-RAY DIFFRACTION93
2.7464-2.81030.27741190.22792589X-RAY DIFFRACTION93
2.8103-2.88050.25121530.212644X-RAY DIFFRACTION94
2.8805-2.95840.24141390.22032603X-RAY DIFFRACTION95
2.9584-3.04540.21531420.21522699X-RAY DIFFRACTION95
3.0454-3.14360.27861380.21442677X-RAY DIFFRACTION96
3.1436-3.25590.27581560.212728X-RAY DIFFRACTION98
3.2559-3.38610.23571280.19652773X-RAY DIFFRACTION98
3.3861-3.54010.21361360.17892774X-RAY DIFFRACTION99
3.5401-3.72650.21431340.16952789X-RAY DIFFRACTION99
3.7265-3.95970.19761330.16152790X-RAY DIFFRACTION99
3.9597-4.2650.19661750.15312783X-RAY DIFFRACTION99
4.265-4.69320.20061310.14392856X-RAY DIFFRACTION99
4.6932-5.37030.18381470.16072840X-RAY DIFFRACTION99
5.3703-6.75790.22711510.18792908X-RAY DIFFRACTION100
6.7579-34.90470.1661410.1633036X-RAY DIFFRACTION99
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)
19.0884-1.4507-4.04612.75970.07492.76960.28310.01710.3518-0.1122-0.0249-0.0196-0.204-0.063-0.28310.3046-0.0226-0.04260.1543-0.01050.108341.359647.476426.2851
22.5712-1.2658-1.29327.52070.3771.1798-0.09810.28230.0789-0.24520.15620.22620.057-0.0857-0.08520.2235-0.0384-0.03320.3152-0.00470.141835.163432.505416.2785
32.97311.3361-0.74682.4635-1.12982.3867-0.30540.3753-0.5136-0.1920.2451-0.25890.3809-0.09130.05080.2786-0.01270.05190.2681-0.08470.268650.813716.979813.8507
42.19940.2888-0.89821.5147-0.91282.2757-0.10660.5508-0.2315-0.39170.1860.02220.08860.0034-0.10150.3183-0.05160.00350.3476-0.06840.199845.999527.4966.3618
54.2882.0221-1.36573.6861-0.63053.094-0.13240.53280.0837-0.28070.10860.22370.0766-0.0512-0.00620.22670.03130.01160.27030.01610.158437.211831.156718.0217
60.6589-1.4256-1.00937.43430.34624.5015-0.11060.2017-0.2930.0713-0.00530.2439-0.0535-0.85750.12130.25150.0345-0.02920.35770.00110.131923.772426.231728.8254
77.68810.2277-5.17951.5522-1.20375.22640.26650.51540.7661-0.11390.0054-0.0316-0.2577-0.1871-0.26740.3033-0.0406-0.01350.2111-0.00170.180150.656946.859213.3068
85.5674-1.19163.9342.77110.2933.44030.19880.75490.2337-0.1729-0.1167-0.33180.24230.4044-0.05210.2517-0.0840.07050.4012-0.01040.238763.529536.39128.2854
93.66752.0207-0.60795.3944-0.64072.653-0.1174-0.1842-0.17940.07650.0257-0.4243-0.02220.35020.02620.22010.0362-0.0310.2741-0.0150.242265.432729.245622.6742
102.3532.49140.59293.45750.47510.3088-0.00410.14580.04880.1230.0112-0.5734-0.01010.19320.01390.251-0.04070.01940.3362-0.00540.259467.779839.502916.663
113.15950.4705-3.1861.70550.10243.42830.0383-0.15580.18660.04150.0604-0.0911-0.07770.0834-0.13010.23080.001-0.0160.1510.00650.178936.149247.065834.1382
121.57710.7162-0.06212.17760.0310.5301-0.0703-0.166-0.0344-0.12170.0722-0.125-0.0421-0.0030.00680.1859-0.0003-0.00480.23250.01420.13941.955131.27342.7303
131.4245-0.00890.13291.66740.19670.3736-0.0016-0.1509-0.24710.02680.08730.09460.0412-0.0499-0.01290.24950.00130.0130.22370.03720.24526.124815.964344.1282
141.23770.5298-0.79585.439-0.09890.73930.0116-0.10350.02970.2813-0.0425-0.1553-0.05020.0138-0.00090.19-0.0101-0.00580.2694-0.01030.16331.033428.491148.9032
152.1262.3284-1.4224.1735-0.76428.45330.0095-0.497-0.24540.2251-0.1531-0.3520.0950.84370.11550.15170.0106-0.01950.29040.00210.235746.043625.086943.8267
161.73813.0203-1.77138.8545-0.45023.976-0.131-0.2348-0.4738-0.3417-0.0606-0.6372-0.22850.93170.24230.3033-0.029-0.0120.39750.03940.178153.302225.970430.0087
173.13330.8544-2.27290.3591-0.1962.99210.284-0.25660.39340.0108-0.13770.1614-0.29570.053-0.28520.3031-0.01620.01740.1941-0.01580.287326.624945.674546.9802
186.98280.09554.32122.1182-1.07744.39490.1386-0.57640.17870.19260.05390.39070.0683-0.4187-0.17990.25980.0120.07250.2331-0.02880.307313.523235.006351.1843
194.7375-2.9772-0.90576.74891.07391.90550.09820.2892-0.1482-0.3592-0.09280.5794-0.0104-0.38-0.0290.2239-0.0422-0.04080.291-0.03170.15911.66328.647736.3804
201.6578-2.5728-0.04815.624-0.93610.52340.0734-0.0576-0.0192-0.0982-0.02390.6632-0.1044-0.1268-0.04180.2512-0.0143-0.00610.27030.00330.24559.419938.750943.1024
217.1649-1.8638-3.4471.59930.06322.4581-0.0163-0.01040.3702-0.19680.1009-0.1483-0.2024-0.136-0.09530.307-0.0256-0.02220.1957-0.0650.230937.653396.499257.9991
221.8615-0.4589-0.43582.9314-0.26361.9633-0.08490.12490.013-0.21060.19260.2936-0.0554-0.2131-0.01780.2341-0.0151-0.04260.2371-0.01030.196531.401881.496648.056
230.8732-0.23370.23462.4086-0.2951.029-0.00640.0886-0.0579-0.18430.0618-0.00820.0527-0.0147-0.03690.2753-0.03860.00550.2352-0.03450.223444.75670.777542.2088
245.89673.2387-0.38915.26170.66344.6852-0.1430.1636-0.0245-0.25180.07330.2575-0.1702-0.15450.06650.22460.0473-0.00110.19560.00970.248833.443380.194449.8256
252.9661-2.3436-1.66134.76731.04386.0074-0.1268-0.2131-0.49410.4205-0.07410.29820.1028-1.07220.18730.2842-0.0305-0.01630.3778-0.04240.229619.171475.425460.6237
266.5456-0.6084-3.32470.55820.15683.55220.00310.43970.5966-0.17990.0887-0.0323-0.151-0.2086-0.19330.3304-0.0491-0.01610.1892-0.00590.271646.875195.818544.9243
276.0937-0.8844.40732.66641.12565.0130.13140.18870.2815-0.0670.0414-0.35540.17410.3318-0.12510.2351-0.05630.07350.2152-0.00530.262859.808685.354639.8567
284.96524.30430.6698.25860.81772.63880.0098-0.2932-0.12690.1634-0.1023-0.4366-0.03630.20460.03970.21920.0272-0.02960.30880.03890.249261.621477.684854.1733
292.5462.36960.10652.6495-0.34610.8740.01190.04180.0447-0.15920.0564-0.558-0.18170.1668-0.05340.2672-0.05360.00730.2686-0.01890.272164.033888.581348.1279
308.2558-0.5274-2.68911.93960.66471.59460.04850.15490.30490.09440.0831-0.1206-0.03760.0203-0.15750.23540.0124-0.03270.2433-0.02170.160232.855696.000566.024
311.23190.4105-0.09421.24950.27510.5586-0.0912-0.1951-0.10090.0960.05260.04550.09180.01310.03560.22050.01110.0140.2675-0.00030.194727.796373.740977.3888
322.2646-1.0037-1.20693.36340.29614.7511-0.0386-0.31220.178-0.06220.0698-0.30280.16350.69220.0340.18350.0072-0.02860.302-0.01830.229145.941474.451167.9897
336.32920.8656-3.46921.0668-0.16074.83640.3931-0.58710.5040.0865-0.13060.0398-0.47980.1232-0.29510.24980.0027-0.0280.1943-0.06590.269922.839694.786578.8189
341.7329-0.69931.96312.5387-0.39293.13630.294-0.5069-0.1333-0.00910.02150.29620.327-0.364-0.22280.19660.0050.03930.41930.00970.29799.493384.453382.865
352.0245-1.1228-0.20295.48650.39412.3633-0.04550.1505-0.2031-0.13320.08060.57530.013-0.3966-0.05650.2243-0.0645-0.03550.3811-0.03030.29987.651278.675767.9245
361.8755-2.67870.01923.77860.12910.58430.02060.02270.027-0.06620.01390.712-0.0746-0.1667-0.03750.24940.00430.00920.3917-0.01870.33735.210488.395974.731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 179 )
5X-RAY DIFFRACTION5chain 'A' and (resid 180 through 210 )
6X-RAY DIFFRACTION6chain 'A' and (resid 211 through 245 )
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 277 )
8X-RAY DIFFRACTION8chain 'A' and (resid 278 through 305 )
9X-RAY DIFFRACTION9chain 'A' and (resid 306 through 342 )
10X-RAY DIFFRACTION10chain 'A' and (resid 343 through 381 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 31 )
12X-RAY DIFFRACTION12chain 'B' and (resid 32 through 69 )
13X-RAY DIFFRACTION13chain 'B' and (resid 70 through 129 )
14X-RAY DIFFRACTION14chain 'B' and (resid 130 through 191 )
15X-RAY DIFFRACTION15chain 'B' and (resid 192 through 209 )
16X-RAY DIFFRACTION16chain 'B' and (resid 210 through 245 )
17X-RAY DIFFRACTION17chain 'B' and (resid 246 through 277 )
18X-RAY DIFFRACTION18chain 'B' and (resid 278 through 305 )
19X-RAY DIFFRACTION19chain 'B' and (resid 306 through 342 )
20X-RAY DIFFRACTION20chain 'B' and (resid 343 through 381 )
21X-RAY DIFFRACTION21chain 'C' and (resid 2 through 31 )
22X-RAY DIFFRACTION22chain 'C' and (resid 32 through 69 )
23X-RAY DIFFRACTION23chain 'C' and (resid 70 through 179 )
24X-RAY DIFFRACTION24chain 'C' and (resid 180 through 210 )
25X-RAY DIFFRACTION25chain 'C' and (resid 211 through 245 )
26X-RAY DIFFRACTION26chain 'C' and (resid 246 through 277 )
27X-RAY DIFFRACTION27chain 'C' and (resid 278 through 305 )
28X-RAY DIFFRACTION28chain 'C' and (resid 306 through 342 )
29X-RAY DIFFRACTION29chain 'C' and (resid 343 through 381 )
30X-RAY DIFFRACTION30chain 'D' and (resid 3 through 31 )
31X-RAY DIFFRACTION31chain 'D' and (resid 32 through 191 )
32X-RAY DIFFRACTION32chain 'D' and (resid 192 through 245 )
33X-RAY DIFFRACTION33chain 'D' and (resid 246 through 277 )
34X-RAY DIFFRACTION34chain 'D' and (resid 278 through 305 )
35X-RAY DIFFRACTION35chain 'D' and (resid 306 through 342 )
36X-RAY DIFFRACTION36chain 'D' and (resid 343 through 382 )

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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

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