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- PDB-4zwl: 2.60 Angstrom resolution crystal structure of betaine aldehyde de... -

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Basic information

Entry
Database: PDB / ID: 4zwl
Title2.60 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) H448F/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-free Cys289
ComponentsBetaine-aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / BetB / structural genomics / NAD / NIAID / National Institute of Allergy and Infectious Diseases / CSGID / Rossmann fold / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHalavaty, A.S. / Minasov, G. / Chen, C. / Joo, J.C. / Yakunin, A.F. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Citation
Journal: To be Published
Title: 2.60 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) H448F/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-free Cys289
Authors: Halavaty, A.S. / Minasov, G. / Chen, C. / Joo, J.C. / Yakunin, A.F. / Anderson, W.F.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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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)463,34931
Polymers456,6018
Non-polymers6,74823
Water21,5281195
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)231,62715
Polymers228,3014
Non-polymers3,32611
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26380 Å2
ΔGint-171 kcal/mol
Surface area62470 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)231,72316
Polymers228,3014
Non-polymers3,42212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26220 Å2
ΔGint-170 kcal/mol
Surface area62530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.140, 170.974, 137.576
Angle α, β, γ (deg.)90.00, 102.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Betaine-aldehyde dehydrogenase /


Mass: 57075.133 Da / Num. of mol.: 8 / Mutation: H448F, Y450L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: betB, SACOL2628 / Plasmid: p15TV-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)/pMAGIC
References: UniProt: Q5HCU0, UniProt: A0A0M3KL40*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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1195 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 7 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, co-crystallized with 5 mM NAD+ against The Classics II G5 (0.2 M lithium sulfate, 0.1 M Tris, pH 8.5, 25% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 123663 / Num. obs: 123663 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.2
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MPB

4mpb


Resolution: 2.6→29.95 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.912 / SU B: 22.761 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 6075 4.9 %RANDOM
Rwork0.15821 ---
obs0.16185 117003 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.908 Å2
Baniso -1Baniso -2Baniso -3
1--4.85 Å20 Å20.04 Å2
2--1.48 Å20 Å2
3---3.05 Å2
Refinement stepCycle: 1 / Resolution: 2.6→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30821 0 427 1195 32443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01932359
X-RAY DIFFRACTIONr_bond_other_d0.0010.0230599
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.97343910
X-RAY DIFFRACTIONr_angle_other_deg0.849370689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3254079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34625.4331491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.777155646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.16615155
X-RAY DIFFRACTIONr_chiral_restr0.1030.24869
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0237023
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027088
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 453 -
Rwork0.238 8528 -
obs--99.99 %
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)
10.74610.0683-0.05150.2812-0.03890.07820.016-0.0278-0.0160.02160.0080.04810.0069-0.0452-0.02390.1586-0.00610.00080.04750.01480.0142-6.9082-8.8042141.4863
20.74610.08840.00490.41730.0210.14220.0527-0.10570.08110.0652-0.0281-0.0383-0.01250.0121-0.02460.158-0.01130.00030.0547-0.00350.019936.24265.0795149.4096
30.5861-0.02780.05550.50180.1350.21910.03920.0892-0.1705-0.08260.0126-0.09660.0270.0531-0.05170.13850.02050.00280.0395-0.02560.073639.8478-24.2716129.1532
40.521-0.00670.0140.3958-0.10040.12250.0230.20670.0548-0.1361-0.0195-0.00490.0580.0011-0.00350.20140.00130.00330.13160.02790.00685.875-0.457109.1832
51.0822-0.126-0.47010.21140.10840.50210.10580.1590.2429-0.006-0.0218-0.0193-0.0831-0.1224-0.0840.15670.02720.02120.07930.02350.0578-4.386356.9589211.4988
61.12460.0391-0.0540.2150.00830.42440.02310.18070.0018-0.01910.0011-0.0225-0.06030.0984-0.02420.143-0.00730.01290.11-0.010.004638.579245.4928200.2034
70.89130.1329-0.15820.1995-0.10240.7923-0.0469-0.0318-0.3722-0.0097-0.0546-0.0590.23510.02190.10150.20220.01840.04920.01850.01670.159925.874216.6953216.638
80.75830.0167-0.0610.13740.05150.4073-0.01430.3661-0.1413-0.0016-0.03860.02440.1044-0.24490.05280.1673-0.05340.00860.3437-0.11440.0432-8.102630.0808188.5559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 496
2X-RAY DIFFRACTION2B-2 - 496
3X-RAY DIFFRACTION3C-2 - 496
4X-RAY DIFFRACTION4D-1 - 496
5X-RAY DIFFRACTION5E1 - 496
6X-RAY DIFFRACTION6F1 - 496
7X-RAY DIFFRACTION7G1 - 496
8X-RAY DIFFRACTION8H1 - 496

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