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- PDB-8uzo: Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from K... -

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Basic information

Entry
Database: PDB / ID: 8uzo
TitleCrystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (ADP bound)
ComponentsBetaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Betaine aldehyde dehydrogenase (BetB)
Function / homology
Function and homology information


betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / metal ion binding
Similarity search - Function
Betaine aldehyde dehydrogenase / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (ADP bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.
History
DepositionNov 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Betaine aldehyde dehydrogenase
B: Betaine aldehyde dehydrogenase
C: Betaine aldehyde dehydrogenase
D: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,05012
Polymers216,2494
Non-polymers1,8018
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22190 Å2
ΔGint-157 kcal/mol
Surface area58450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.801, 100.578, 123.753
Angle α, β, γ (deg.)90.00, 95.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Betaine aldehyde dehydrogenase


Mass: 54062.281 Da / Num. of mol.: 4 / Mutation: V62A, Q485P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Strain: KCTC 2190 / Gene: betB_3 / Plasmid: KlaeA.00020.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A447LC14
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JCSG+ G8: 20% PEG 3350, 0.15 M DL-malic acid, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. Overnight soak in 20mM ADP in crystallant. Plate: 13677, well G8 drop 1. Puck: PSL-0505, Cryo: 30% PEG3350 + 70% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 9, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→123.1 Å / Num. obs: 118414 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.043 / Rrim(I) all: 0.084 / Χ2: 0.98 / Net I/σ(I): 10.3 / Num. measured all: 440006
Reflection shellResolution: 2.1→2.15 Å / % possible obs: 99.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.748 / Num. measured all: 33842 / Num. unique obs: 8728 / CC1/2: 0.778 / Rpim(I) all: 0.436 / Rrim(I) all: 0.867 / Χ2: 0.98 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→83.36 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 5848 4.94 %
Rwork0.1867 --
obs0.188 118275 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→83.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14757 0 112 519 15388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515375
X-RAY DIFFRACTIONf_angle_d0.75320930
X-RAY DIFFRACTIONf_dihedral_angle_d12.895692
X-RAY DIFFRACTIONf_chiral_restr0.0482370
X-RAY DIFFRACTIONf_plane_restr0.0112731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.31961930.28223735X-RAY DIFFRACTION99
2.12-2.150.31811760.27063772X-RAY DIFFRACTION99
2.15-2.180.32862250.26463655X-RAY DIFFRACTION99
2.18-2.20.32711940.26163755X-RAY DIFFRACTION99
2.2-2.230.29352020.25483693X-RAY DIFFRACTION99
2.23-2.260.28511960.25273755X-RAY DIFFRACTION100
2.26-2.290.30931990.25093773X-RAY DIFFRACTION100
2.29-2.330.2642070.23893710X-RAY DIFFRACTION99
2.33-2.370.29621960.23613706X-RAY DIFFRACTION99
2.37-2.40.30642040.23753740X-RAY DIFFRACTION99
2.4-2.450.26341850.22793777X-RAY DIFFRACTION100
2.45-2.490.28341800.21623759X-RAY DIFFRACTION100
2.49-2.540.26831750.21373787X-RAY DIFFRACTION100
2.54-2.590.2532050.20533715X-RAY DIFFRACTION99
2.59-2.650.25781940.20693740X-RAY DIFFRACTION99
2.65-2.710.25381980.21083750X-RAY DIFFRACTION100
2.71-2.780.26041750.21483768X-RAY DIFFRACTION100
2.78-2.850.24571960.22183745X-RAY DIFFRACTION99
2.85-2.930.27551920.22983740X-RAY DIFFRACTION100
2.93-3.030.29261860.22953771X-RAY DIFFRACTION99
3.03-3.140.24462050.21743735X-RAY DIFFRACTION99
3.14-3.260.23971900.21513775X-RAY DIFFRACTION99
3.26-3.410.22732020.20433678X-RAY DIFFRACTION99
3.41-3.590.22281950.1963747X-RAY DIFFRACTION99
3.59-3.820.20131810.17633765X-RAY DIFFRACTION98
3.82-4.110.17631720.15123722X-RAY DIFFRACTION98
4.11-4.520.12282130.12553737X-RAY DIFFRACTION99
4.52-5.180.13352000.12213781X-RAY DIFFRACTION99
5.18-6.520.18432120.15643807X-RAY DIFFRACTION99
6.52-83.360.15462000.14823834X-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)
10.0459-0.0723-0.03340.11510.05110.0404-0.0321-0.0218-0.2896-0.1327-0.0877-0.31720.12640.3532-0.00010.34380.00670.06450.4040.03450.427793.4256-14.021619.4222
20.07220.0098-0.12110.1434-0.00210.2838-0.0519-0.0288-0.1188-0.1221-0.0996-0.12690.03030.1344-0.00020.3133-0.0104-0.02140.32760.00950.354483.0384-11.550422.5991
30.09330.0345-0.05890.0635-0.06270.06760.17010.02040.0516-0.0584-0.06140.1529-0.10090.05220.00940.4102-0.0633-0.03710.3736-0.0350.35976.62317.375425.7206
40.10610.0874-0.04730.19930.02840.16690.1241-0.09710.2027-0.0149-0.0205-0.0235-0.32820.1550.05850.4546-0.09620.03380.28770.00980.38278.779717.771430.8669
50.1264-0.011-0.12990.00110.00910.1308-0.03030.1229-0.0955-0.0616-0.05550.0015-0.0516-0.1118-00.3299-0.0185-0.0260.3096-0.02660.327365.9398-12.2120.6629
60.06510.07540.07110.09570.08960.0793-0.02540.2229-0.1-0.06810.06940.3392-0.0178-0.2321-0.00030.2961-0.07060.03410.4503-0.03310.499126.522-24.677937.3669
70.06630.0539-0.07310.2103-0.03390.0805-0.0830.1264-0.12390.0241-0.00630.0890.0499-0.2296-0.00010.3073-0.0328-0.00630.365-0.02610.391236.9893-20.846737.8606
80.05620.027-0.0180.01830.01210.07620.0045-0.1858-0.03260.03350.040.0248-0.0150.023600.34130.02910.02830.3428-0.00670.380643.6282-9.790753.6647
90.0696-0.0586-0.05250.05140.05480.06890.0202-0.31630.11760.2205-0.03290.1919-0.1086-0.220600.38850.05560.05930.4713-0.0090.374933.43511.191461.7244
100.20480.0552-0.0870.14080.08290.1142-0.0632-0.1538-0.07180.06830.0385-0.00220.0183-0.06570.00170.35570.0026-0.0070.38450.01770.322250.7746-10.650151.1597
110.0891-0.0933-0.04190.10190.04110.0222-0.00060.2740.0848-0.1199-0.03250.0332-0.1302-0.1083-0.09960.48050.1978-0.00050.76930.18240.299145.62454.1162-6.5583
120.0273-0.017-0.00980.03850.03740.03580.09790.15540.20210.0352-0.0773-0.003-0.1373-0.336700.33310.0603-0.0020.45520.05610.358546.35012.07415.4746
130.3176-0.0341-0.21340.16220.12020.21160.09230.30950.01250.0132-0.0588-0.042-0.0176-0.22080.18060.25810.04-0.04110.48360.02040.217351.4173-4.823610.1316
140.3324-0.16920.19160.0869-0.09840.1158-0.07440.3199-0.056-0.0565-0.11860.06370.0608-0.2048-0.13210.4067-0.06140.00980.6119-0.20320.39361.3234-19.90510.5284
150.02510.0191-0.00990.0168-0.00640.0058-0.05890.1546-0.1159-0.14430.0326-0.00460.049-0.2485-0.03430.5126-0.09880.01350.8526-0.35360.431352.1461-31.0566-9.4834
160.00620.01310.00790.0376-0.00690.0746-0.0370.1341-0.0834-0.0308-0.0060.0226-0.0438-0.0814-0.1030.5501-0.05970.020.9077-0.26190.324758.7213-21.405-19.1198
170.1840.22180.05880.40270.0170.0464-0.02620.3938-0.2754-0.0527-0.0396-0.13110.1159-0.1668-0.12570.4389-0.05610.06810.5527-0.25240.438465.4299-28.9538-2.1271
180.13160.0657-0.09470.0313-0.0460.0675-0.09780.1339-0.0557-0.09220.0120.0326-0.1728-0.02600.2756-0.0347-0.03320.315-0.02840.25563.8134-9.814921
190.00010.0034-0.00040.0283-0.03040.05120.0163-0.0836-0.0811-0.0582-0.0084-0.0070.2477-0.03040.02580.5723-0.0177-0.03880.71260.37260.474274.3794-40.777364.0741
200.02090.0038-0.01540.31330.05480.0781-0.0319-0.4561-0.17520.0482-0.0722-0.1725-0.046-0.09910.01080.34330.0462-0.02660.60560.11790.353373.945-22.021853.0833
210.1240.04930.14080.2385-0.06090.32420.0208-0.2579-0.1218-0.0409-0.0387-0.02390.1022-0.0162-0.33030.33380.05280.01040.25090.19010.374969.4226-28.338343.8747
220.05570.020.04980.0330.01020.0470.0796-0.3522-0.18270.106-0.09770.0250.1259-0.1026-0.03390.3807-0.036-0.03010.72550.27290.470367.9637-31.685356.7211
230.8254-0.06520.56310.0105-0.03030.42240.0346-0.2427-0.2928-0.07310.12320.02470.3093-0.24560.20580.7059-0.11960.02230.27180.12560.78859.0324-44.849939.465
240.0584-0.0553-0.03080.05220.03010.0164-0.1431-0.0276-0.19410.0301-0.02290.06270.18930.0268-0.29571.1609-0.05470.00720.33230.18971.112768.5398-58.582233.4616
250.00470.01740.00930.06190.03210.01660.0436-0.0235-0.01730.0307-0.0122-0.00710.0413-0.01690.11661.3237-0.18290.0720.52420.36291.186561.9904-63.287546.2426
260.0318-0.04420.00630.0625-0.00610.0296-0.06640.0057-0.14520.1277-0.00350.00590.1092-0.0359-0.12130.9844-0.3591-0.00320.45040.17941.058855.2194-56.655736.1859
270.1692-0.17610.23750.5389-0.13810.4195-0.0617-0.0928-0.19480.13690.05270.09880.1519-0.2203-0.02350.3121-0.11210.03810.21140.04970.465655.8047-29.733234.6753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 230 )
3X-RAY DIFFRACTION3chain 'A' and (resid 231 through 290 )
4X-RAY DIFFRACTION4chain 'A' and (resid 291 through 441 )
5X-RAY DIFFRACTION5chain 'A' and (resid 442 through 490 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 81 )
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 230 )
8X-RAY DIFFRACTION8chain 'B' and (resid 231 through 290 )
9X-RAY DIFFRACTION9chain 'B' and (resid 291 through 363 )
10X-RAY DIFFRACTION10chain 'B' and (resid 364 through 490 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 42 )
12X-RAY DIFFRACTION12chain 'C' and (resid 43 through 81 )
13X-RAY DIFFRACTION13chain 'C' and (resid 82 through 230 )
14X-RAY DIFFRACTION14chain 'C' and (resid 231 through 290 )
15X-RAY DIFFRACTION15chain 'C' and (resid 291 through 330 )
16X-RAY DIFFRACTION16chain 'C' and (resid 331 through 363 )
17X-RAY DIFFRACTION17chain 'C' and (resid 364 through 441 )
18X-RAY DIFFRACTION18chain 'C' and (resid 442 through 490 )
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 42 )
20X-RAY DIFFRACTION20chain 'D' and (resid 43 through 81 )
21X-RAY DIFFRACTION21chain 'D' and (resid 82 through 168 )
22X-RAY DIFFRACTION22chain 'D' and (resid 169 through 230 )
23X-RAY DIFFRACTION23chain 'D' and (resid 231 through 290 )
24X-RAY DIFFRACTION24chain 'D' and (resid 291 through 330 )
25X-RAY DIFFRACTION25chain 'D' and (resid 331 through 363 )
26X-RAY DIFFRACTION26chain 'D' and (resid 364 through 409 )
27X-RAY DIFFRACTION27chain 'D' and (resid 410 through 490 )

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