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- PDB-4mpb: 1.7 Angstrom resolution crystal structure of betaine aldehyde deh... -

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Basic information

Entry
Database: PDB / ID: 4mpb
Title1.7 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus
ComponentsBetaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / structural genomics / NAD / Center for Structural Genomics of Infectious / NIAID / National Institute of Allergy and Infectious Diseases / CSGID / Rossmann fold / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


cellular response to chemical stimulus / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / nucleotide binding / metal ion binding
Similarity search - Function
Betaine aldehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 ...Betaine aldehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Betaine aldehyde dehydrogenase / Betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsHalavaty, A.S. / Shuvalova, L. / Minasov, G. / Dubrovska, I. / Winsor, J. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Citation
Journal: Appl.Environ.Microbiol. / Year: 2014
Title: Structure-based mutational studies of substrate inhibition of betaine aldehyde dehydrogenase BetB from Staphylococcus aureus.
Authors: Chen, C. / Joo, J.C. / Brown, G. / Stolnikova, E. / Halavaty, A.S. / Savchenko, A. / Anderson, W.F. / Yakunin, A.F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus
Authors: Halavaty, A.S. / Rich, R.L. / Chen, C. / Joo, J.C. / Minasov, G. / Dubrovska, I. / Winsor, J.R. / Myszka, D.G. / Duban, M. / Shuvalova, L. / Yakunin, A.F. / Anderson, W.F.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionSep 25, 2013ID: 3ED6
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Other
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3May 13, 2015Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1668
Polymers115,0092
Non-polymers1576
Water23,7081316
1
A: Betaine aldehyde dehydrogenase
hetero molecules

A: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,22610
Polymers115,0092
Non-polymers2178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7940 Å2
ΔGint-77 kcal/mol
Surface area34640 Å2
MethodPISA
2
B: Betaine aldehyde dehydrogenase
hetero molecules

B: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1066
Polymers115,0092
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7850 Å2
ΔGint-62 kcal/mol
Surface area34930 Å2
MethodPISA
3
A: Betaine aldehyde dehydrogenase
B: Betaine aldehyde dehydrogenase
hetero molecules

A: Betaine aldehyde dehydrogenase
B: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,33216
Polymers230,0184
Non-polymers31412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area21370 Å2
ΔGint-149 kcal/mol
Surface area63990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.313, 118.570, 87.947
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 Betaine aldehyde dehydrogenase


Mass: 57504.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: betB, SACOL2628 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5HCU0, UniProt: A0A0H2X0S3*PLUS, betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1316 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1:1 v/v JCSG+ Suite condition 42 to 7.4 mg/mL protein (in 0.5 M sodium chloride, 5 mM BME, 10 mM Tris-HCl, pH 8.3), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2008 / Details: beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→88.05 Å / Num. all: 122661 / Num. obs: 122661 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.89
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.5 / Num. unique all: 12121 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.7→19.79 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.483 / SU ML: 0.058 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17531 6146 5 %RANDOM
Rwork0.13842 ---
obs0.14027 116223 99.86 %-
all-116223 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.893 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.66 Å2-0 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7806 0 6 1316 9128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198729
X-RAY DIFFRACTIONr_bond_other_d0.0010.028313
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.95511912
X-RAY DIFFRACTIONr_angle_other_deg0.98319261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.03951164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02625.588408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39151572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3631541
X-RAY DIFFRACTIONr_chiral_restr0.1060.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210413
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021956
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 461 -
Rwork0.255 8449 -
obs-8449 99.89 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.68472.15-0.75813.2201-0.08981.05550.288-0.3664-0.157-0.1749-0.2632-0.65960.04270.2816-0.02480.2040.06030.14120.12430.0310.239286.852-16.009977.208
22.54481.2261-0.88212.5172-0.09060.66890.00080.2771-0.1036-0.4391-0.0484-0.28550.0869-0.00620.04760.28020.08040.1380.10640.00750.098180.0481-14.120367.3163
31.05630.11690.21780.8181-0.02651.01530.02140.023-0.1542-0.1531-0.02920.01110.1113-0.06040.00780.11780.01460.03530.0144-0.00990.064862.8562-19.85286.4135
41.83950.4538-1.43113.1466-2.29594.17950.0279-0.06630.0244-0.2336-0.1798-0.3946-0.02060.19460.15190.09130.02420.09770.02280.02190.137984.9112-8.53185.6763
511.86488.3913-4.53116.5796-3.49743.96240.3087-0.23890.07350.1478-0.2734-0.2458-0.18390.2483-0.03530.1010.010.10570.0380.03810.207285.9649-0.807986.8907
65.77891.4438-2.29822.0876-0.35492.49720.03160.01920.1283-0.17020.00450.05370.0213-0.0313-0.03620.06670.01540.02750.00660.01260.032568.8238-7.267494.8272
78.0298-0.98520.74960.6029-0.66271.0951-0.0735-0.0130.12530.07210.03170.04230.0515-0.05230.04180.10370.00680.00140.0507-0.03090.085339.5171-9.003998.7919
80.7722-0.3451-0.16740.2971-0.24530.97960.08350.01050.1431-0.1206-0.03-0.0455-0.00220.0212-0.05350.21580.02460.04180.0768-0.02650.111767.1664-6.721680.8129
91.0113-0.3058-0.11460.9486-0.18780.53460.05450.1104-0.0447-0.2666-0.0777-0.06730.07590.02540.02320.15420.02750.05680.0255-0.00850.039968.8229-12.951277.7738
101.93540.14180.93870.61580.40981.09370.03690.19130.1193-0.2412-0.0484-0.0195-0.0329-0.03130.01150.17530.02080.02660.05910.0060.03858.6915-0.736871.0396
111.0491-0.2576-0.09481.54910.61051.07830.0063-0.01960.0591-0.18610.0035-0.2023-0.02660.0783-0.00990.1238-0.0110.08530.03020.02330.102179.134518.903784.5935
120.90670.6162-0.43353.369-0.19670.6042-0.10570.1090.0538-0.4520.0475-0.1859-0.05640.01220.05820.154-0.02230.07450.0260.02470.120878.23925.100781.1677
132.1364-1.18-0.33252.55010.24990.51490.18060.13270.0484-0.4727-0.1099-0.5613-0.0380.0339-0.07070.24050.03430.19670.09830.04610.217388.909510.247775.2312
145.9648-1.006-1.29942.4334-1.80962.1940.13550.9170.1652-0.5332-0.2705-0.26630.2562-0.03350.1350.53780.0420.24350.27710.07650.219684.348117.463165.4812
153.7076-1.4584-0.63923.41590.18330.29990.16470.33370.3852-0.4839-0.1239-0.5899-0.06320.1015-0.04090.30810.04090.21880.18360.08630.195487.255814.418269.8896
163.6439-1.7191-1.10033.12340.61491.06360.02790.27660.0633-0.481-0.1069-0.18350.0470.03910.0790.27880.00750.09410.06050.04340.070473.40221.03173.5482
171.01590.22520.24050.92290.03470.43970.0145-0.00630.1343-0.1479-0.0228-0.0031-0.04170.01550.00830.10550.00140.03780.00790.00750.041867.517920.307987.0182
180.9904-0.53980.89420.6386-0.3441.6016-0.0544-0.0260.0288-0.1537-0.0022-0.06520.0146-0.12880.05660.1333-0.00510.0270.02610.00970.060364.22366.20784.9962
194.22874.61491.29195.07671.04133.76970.0168-0.06720.11350.0215-0.06680.1201-0.0205-0.11670.050.10720.02650.01160.0350.01140.080259.638-4.088189.1564
201.1554-0.15370.89311.3512-0.30180.79470.0767-0.2471-0.1416-0.10310.00020.2716-0.004-0.1749-0.0770.1166-0.0036-0.06170.10480.00180.153127.6628-14.651292.5616
2113.3778-17.649-3.004129.0605-2.08537.01230.30650.4516-0.0863-0.1633-0.5732-0.1639-0.3406-0.12870.26670.16770.0762-0.07460.2056-0.00770.280882.4529-34.3031124.4494
222.551-0.61520.1632.7372-0.04340.3461-0.0506-0.2702-0.06660.1372-0.0226-0.3689-0.03180.23810.07310.0610.0106-0.05450.24430.05850.097282.8331-13.7038129.9656
231.0194-0.09250.44612.2032-0.6740.5578-0.0903-0.2812-0.11960.20180.1437-0.1446-0.0215-0.0651-0.05340.08670.0475-0.02580.17970.03290.064974.8621-15.397133.2951
241.11210.19651.51961.15232.23295.6836-0.02880.01990.1013-0.10440.0604-0.1135-0.23110.2454-0.03160.0664-0.0226-0.01450.09610.02320.099575.66684.5154114.9042
250.84270.1237-0.39736.7578-2.22861.46610.0423-0.0105-0.023-0.0932-0.1842-0.21620.050.17490.14190.03340.02370.01420.03380.02130.028275.4748-12.7254107.9281
260.9560.0837-0.0122.7165-2.0722.1578-0.003-0.1118-0.1582-0.0903-0.0354-0.07840.12790.05980.03840.03220.01460.00820.02710.03260.048368.762-21.0738113.5549
273.1905-3.184-0.33835.61620.1591.146-0.0390.15770.0579-0.0398-0.02420.1033-0.07580.06410.06310.0527-0.003-0.01360.03740.00150.039655.506716.1314102.9823
280.6118-0.3620.14240.2930.0880.64020.0042-0.0582-0.043-0.0071-0.01820.01410.0101-0.01580.01410.040.0136-0.00930.0890.02990.041765.1208-9.9067121.0014
291.1082-0.34560.28090.99830.04120.8487-0.0485-0.1283-0.01830.03380.0221-0.08380.02520.08020.02640.02080.0137-0.00680.06430.0290.028173.6222-10.8668122.1025
301.3682-0.2212-0.24430.77980.39711.0444-0.093-0.3140.00150.21510.08430.01230.01760.00020.00870.08180.0308-0.01720.11250.01650.038163.1516-4.2304131.0509
310.58410.46090.55291.22110.71630.79210.034-0.1924-0.04540.1326-0.04390.03210.0568-0.10850.00990.0527-0.0004-0.00060.08870.0280.034851.6824-10.7798126.4892
322.843-0.18781.15890.9738-0.24981.23910.0527-0.1488-0.2113-0.0180.01240.00570.1273-0.0248-0.0650.078-0.0318-0.01710.0470.06390.11947.363-31.6742118.1612
338.10360.9121.35951.0199-0.13260.57470.1297-0.3053-0.7845-0.0138-0.00930.00010.1706-0.0597-0.12030.1474-0.0347-0.0590.06040.110.263451.1362-40.7781120.9907
344.5069-0.4158-2.58661.1347-0.05411.6140.033-0.6063-0.08840.0412-0.0752-0.14320.03310.25850.04220.1803-0.0971-0.06420.44670.14190.180555.3615-30.2975135.9079
354.8981.1072-1.92420.50030.01161.9275-0.1194-0.885-0.96990.1801-0.2172-0.14690.39430.1210.33660.2356-0.00910.0220.31340.29630.347151.3069-39.4712134.1051
3611.305-0.0441.11510.06450.04460.41540.1877-0.7105-0.80950.0421-0.0748-0.05780.2237-0.1241-0.1130.1444-0.0508-0.03220.18620.19270.211556.8545-38.3041131.8337
371.1811-0.0629-0.38031.50540.12480.76630.0613-0.3214-0.02910.1309-0.073-0.01550.1223-0.03090.01170.075-0.0590.00580.18350.08090.103741.346-27.094127.8759
380.69060.02310.23671.0184-0.06170.60740.0419-0.1176-0.0722-0.0235-0.01060.11080.0538-0.1065-0.03130.0269-0.01310.00150.04510.02320.032844.1205-19.149115.2475
391.90013.02150.25197.66070.58072.7981-0.13340.0250.1401-0.13140.06310.1186-0.034-0.03660.07030.02960.01130.00240.03760.01390.045559.3845-5.1005112.3655
401.38360.1095-0.47560.76280.18131.44470.1413-0.00820.2983-0.2766-0.03750.0265-0.16120.0023-0.10380.13010.00280.01620.0544-0.00650.12855.890428.0568109.4269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 15
2X-RAY DIFFRACTION2A16 - 48
3X-RAY DIFFRACTION3A49 - 80
4X-RAY DIFFRACTION4A81 - 100
5X-RAY DIFFRACTION5A101 - 110
6X-RAY DIFFRACTION6A111 - 126
7X-RAY DIFFRACTION7A127 - 143
8X-RAY DIFFRACTION8A144 - 163
9X-RAY DIFFRACTION9A164 - 233
10X-RAY DIFFRACTION10A234 - 257
11X-RAY DIFFRACTION11A258 - 287
12X-RAY DIFFRACTION12A288 - 308
13X-RAY DIFFRACTION13A309 - 339
14X-RAY DIFFRACTION14A340 - 363
15X-RAY DIFFRACTION15A364 - 382
16X-RAY DIFFRACTION16A383 - 404
17X-RAY DIFFRACTION17A405 - 449
18X-RAY DIFFRACTION18A450 - 466
19X-RAY DIFFRACTION19A467 - 478
20X-RAY DIFFRACTION20A479 - 496
21X-RAY DIFFRACTION21B-4 - 3
22X-RAY DIFFRACTION22B4 - 24
23X-RAY DIFFRACTION23B25 - 56
24X-RAY DIFFRACTION24B57 - 69
25X-RAY DIFFRACTION25B70 - 87
26X-RAY DIFFRACTION26B88 - 126
27X-RAY DIFFRACTION27B127 - 143
28X-RAY DIFFRACTION28B144 - 164
29X-RAY DIFFRACTION29B165 - 214
30X-RAY DIFFRACTION30B215 - 238
31X-RAY DIFFRACTION31B239 - 266
32X-RAY DIFFRACTION32B267 - 299
33X-RAY DIFFRACTION33B300 - 327
34X-RAY DIFFRACTION34B328 - 349
35X-RAY DIFFRACTION35B350 - 363
36X-RAY DIFFRACTION36B364 - 379
37X-RAY DIFFRACTION37B380 - 405
38X-RAY DIFFRACTION38B406 - 466
39X-RAY DIFFRACTION39B467 - 477
40X-RAY DIFFRACTION40B478 - 496

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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