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- PDB-4mpy: 1.85 Angstrom resolution crystal structure of betaine aldehyde de... -

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Basic information

Entry
Database: PDB / ID: 4mpy
Title1.85 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus (IDP00699) in complex with NAD+
ComponentsBetaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / structural genomics / NAD / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / Rossmann fold
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Betaine aldehyde dehydrogenase / Betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHalavaty, A.S. / Minasov, G. / Shuvalova, L. / 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 14, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionOct 9, 2013ID: 3FG0
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Nov 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
C: Betaine aldehyde dehydrogenase
D: Betaine aldehyde dehydrogenase
E: Betaine aldehyde dehydrogenase
F: Betaine aldehyde dehydrogenase
G: Betaine aldehyde dehydrogenase
H: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,78135
Polymers460,0378
Non-polymers5,74427
Water82,4014574
1
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)232,85616
Polymers230,0184
Non-polymers2,83812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26210 Å2
ΔGint-204 kcal/mol
Surface area60920 Å2
MethodPISA
2
E: Betaine aldehyde dehydrogenase
F: Betaine aldehyde dehydrogenase
G: Betaine aldehyde dehydrogenase
H: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,92519
Polymers230,0184
Non-polymers2,90715
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26070 Å2
ΔGint-196 kcal/mol
Surface area60740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.866, 159.146, 122.993
Angle α, β, γ (deg.)90.00, 94.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Betaine aldehyde dehydrogenase


Mass: 57504.582 Da / Num. of mol.: 8
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4574 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1:1 v/v PEGsII Suite (condition D10) and protein (7.4 mg/mL in 0.25 M sodium chloride, 5 mM BME, 10 mM Tris-HCl, pH 8.3, 2 mM NAD+), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2008 / Details: K-B mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. all: 324147 / Num. obs: 324147 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.84
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.21 / Num. unique all: 16115 / % 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: MOLECULAR REPLACEMENT / Resolution: 1.85→24.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.292 / SU ML: 0.069 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16675 9843 3 %RANDOM
Rwork0.12564 ---
obs0.12688 314222 99.71 %-
all-314222 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.214 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å20.67 Å2
2---0.49 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31059 0 371 4574 36004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01933382
X-RAY DIFFRACTIONr_bond_other_d0.0010.0231453
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.97245246
X-RAY DIFFRACTIONr_angle_other_deg0.834372782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.71154262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74425.5171528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88155831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.59815152
X-RAY DIFFRACTIONr_chiral_restr0.1050.24974
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0238513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027323
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 739 -
Rwork0.17 22471 -
obs-22471 97.04 %
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)
10.36750.00870.16230.2124-0.05160.5064-0.06910.04470.08010.0317-0.0308-0.076-0.12660.17080.09990.0405-0.0463-0.04480.06330.04130.068539.813736.629267.5564
20.2802-0.1121-0.0040.2792-0.06940.485-0.01540.0713-0.02-0.0422-0.034-0.02560.05330.06390.04940.0208-0.0020.00590.03340.00130.016923.733116.730843.0362
30.23380.0337-0.06280.224-0.07130.2681-0.0218-0.0718-0.01210.0166-0.0084-0.0399-0.01650.0150.03020.02710.0129-0.01530.023600.01484.763617.573190.0972
40.1491-0.0197-0.05290.3055-0.1530.3289-0.0020.02090.01720.04220.01930.0426-0.0894-0.0659-0.01730.04550.0206-0.01290.0150.00020.0212-10.664637.588865.1228
50.2404-0.0179-0.01580.2297-0.02660.3231-0.0029-0.0371-0.02640.0361-0.00860.01120.0224-0.00660.01150.019-0.0086-0.01220.01170.01230.0237-30.66075.872424.0791
60.20110.00750.00340.1595-0.00320.22390.00210.03370.0025-0.0441-0.00310.0217-0.0141-0.03220.0010.02870.0031-0.02140.01950.00160.0185-28.44029.3185-10.9514
70.3211-0.0708-0.03330.30420.02040.12050.0155-0.01430.04710.007-0.01230.0865-0.0441-0.0162-0.00320.03160.0094-0.01010.0114-0.00910.0604-45.326248.612315.9139
80.2680.08430.0280.22540.08650.13660.00890.00670.0203-0.0340.013-0.0209-0.0530.0116-0.02190.0364-0.0116-0.00940.00490.00850.0358-11.344548.63574.8801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 496
2X-RAY DIFFRACTION2B-3 - 496
3X-RAY DIFFRACTION3C-6 - 496
4X-RAY DIFFRACTION4D-1 - 496
5X-RAY DIFFRACTION5E-4 - 496
6X-RAY DIFFRACTION6F-1 - 496
7X-RAY DIFFRACTION7G-6 - 496
8X-RAY DIFFRACTION8H-3 - 496

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