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- PDB-4nu9: 2.30 Angstrom resolution crystal structure of betaine aldehyde de... -

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Basic information

Entry
Database: PDB / ID: 4nu9
Title2.30 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus with BME-free Cys289
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


betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / 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, C-terminal / Aldehyde dehydrogenase, N-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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Stam, J. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: 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
DepositionDec 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)114,9496
Polymers114,8572
Non-polymers924
Water10,899605
1
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)229,89812
Polymers229,7144
Non-polymers1848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area21730 Å2
ΔGint-178 kcal/mol
Surface area62250 Å2
MethodPISA
2
A: Betaine aldehyde dehydrogenase
hetero molecules

A: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9496
Polymers114,8572
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area8120 Å2
ΔGint-82 kcal/mol
Surface area33780 Å2
MethodPISA
3
B: Betaine aldehyde dehydrogenase
hetero molecules

B: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9496
Polymers114,8572
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area8050 Å2
ΔGint-86 kcal/mol
Surface area34030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.639, 118.427, 88.532
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 / betB


Mass: 57428.457 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/magic
References: UniProt: Q5HCU0, UniProt: A0A0H2X0S3*PLUS, betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 605 / 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: 49.46 %
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, crystallized using the JCSG+ Suite (D6: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG8000), VAPOR ...Details: 7 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, crystallized using the JCSG+ Suite (D6: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG8000), 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: Nov 18, 2013 / 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: 2.3→30 Å / Num. all: 48647 / Num. obs: 48647 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 18.37
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2474 / % 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
Starting model: PDB ENTRY 4MPB

4mpb


Resolution: 2.3→29.87 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.515 / SU ML: 0.134 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21538 2469 5.1 %RANDOM
Rwork0.15934 ---
obs0.16215 46132 96.43 %-
all-46132 --
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: 25.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---1.94 Å2-0 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7729 0 4 605 8338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197960
X-RAY DIFFRACTIONr_bond_other_d0.0010.027580
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.95510781
X-RAY DIFFRACTIONr_angle_other_deg0.849317501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.92151013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25125.418371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.649151400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8771537
X-RAY DIFFRACTIONr_chiral_restr0.1030.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021750
LS refinement shellResolution: 2.3→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 199 -
Rwork0.194 3244 -
obs-3244 93.99 %
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)
10.60460.235-0.21191.6835-0.60291.0439-0.02950.10930.0563-0.0258-0.003-0.1424-0.07230.1160.03250.0254-0.0314-0.00950.15470.01810.0349127.9522133.815999.8324
20.72960.5093-0.13950.7872-0.00730.0732-0.04250.06160.0205-0.06180.03-0.0195-0.01630.02470.01250.0835-0.0138-0.0010.15640.00910.0308119.1401123.732298.0644
32.55790.0736-0.36390.9399-0.1930.7216-0.00740.27850.2935-0.01840.03110.0352-0.1735-0.0764-0.02370.14520.023-0.00750.1480.080.102102.6104151.801594.0989
40.7637-0.0132-0.03151.3443-0.45661.2225-0.00210.07590.0390.02440.03390.1265-0.1101-0.1348-0.03180.05590.0137-0.00290.10860.01890.016598.0027136.4733105.5897
50.91821.01410.38242.55310.94490.35980.0413-0.0235-0.150.1659-0.03780.0910.08280.0057-0.00340.18910.00370.00770.1858-0.01720.165110.789797.0207110.2033
61.2881-0.25140.12331.2068-0.07510.81030.0431-0.07320.06550.2596-0.0368-0.2212-0.05630.0305-0.00630.1865-0.045-0.10580.05170.01080.0743129.0022132.2724139.6131
70.7433-0.01060.0170.4924-0.15130.3886-0.0135-0.0981-0.00330.243-0.0225-0.0902-0.07180.0480.03610.1928-0.0014-0.04370.0741-0.00770.0203116.3243127.858140.9872
81.08520.17620.22231.75480.08361.1008-0.0165-0.0717-0.06410.2408-0.0379-0.21470.0370.08630.05440.18830.0277-0.13010.11530.0220.1119135.8079101.7446145.7642
91.3029-0.17950.08581.4463-0.41050.84890.0066-0.0148-0.12020.10760.0149-0.02630.05780.0394-0.02140.1354-0.0002-0.04330.06410.00740.0252119.841102.848134.0048
105.66940.3187-1.07110.12350.10950.5702-0.00750.2202-0.10620.0575-0.01550.06710.0406-0.12770.0230.2547-0.00020.05740.13290.00670.203488.6163130.8555129.4379
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 129
2X-RAY DIFFRACTION2A130 - 257
3X-RAY DIFFRACTION3A258 - 403
4X-RAY DIFFRACTION4A404 - 472
5X-RAY DIFFRACTION5A473 - 496
6X-RAY DIFFRACTION6B1 - 126
7X-RAY DIFFRACTION7B127 - 257
8X-RAY DIFFRACTION8B258 - 401
9X-RAY DIFFRACTION9B402 - 472
10X-RAY DIFFRACTION10B473 - 496

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