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- PDB-4q92: 1.90 Angstrom resolution crystal structure of apo betaine aldehyd... -

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Basic information

Entry
Database: PDB / ID: 4q92
Title1.90 Angstrom resolution crystal structure of apo betaine aldehyde dehydrogenase (betB) G234S mutant from Staphylococcus aureus (IDP00699) with BME-modified 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
DI(HYDROXYETHYL)ETHER / Betaine-aldehyde dehydrogenase / Betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)
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
DepositionApr 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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_ncs_dom_lim / 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_alt_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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)229,23912
Polymers228,8894
Non-polymers3508
Water28,6621591
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21630 Å2
ΔGint-141 kcal/mol
Surface area62490 Å2
MethodPISA
2
A: Betaine aldehyde dehydrogenase
B: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6206
Polymers114,4452
Non-polymers1754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-67 kcal/mol
Surface area33770 Å2
MethodPISA
3
C: Betaine aldehyde dehydrogenase
D: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6206
Polymers114,4452
Non-polymers1754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-70 kcal/mol
Surface area34440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.363, 156.438, 88.417
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-768-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYSAA0 - 49621 - 517
21GLYGLYLYSLYSBB0 - 49621 - 517
12METMETSERSERAA1 - 49522 - 516
22METMETSERSERCC1 - 49522 - 516
13GLYGLYSERSERAA0 - 49521 - 516
23GLYGLYSERSERDD0 - 49521 - 516
14METMETSERSERBB1 - 49522 - 516
24METMETSERSERCC1 - 49522 - 516
15GLYGLYSERSERBB0 - 49521 - 516
25GLYGLYSERSERDD0 - 49521 - 516
16METMETSERSERCC1 - 49522 - 516
26METMETSERSERDD1 - 49522 - 516

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Betaine aldehyde dehydrogenase


Mass: 57222.273 Da / Num. of mol.: 4 / Mutation: G234S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: betB, SACOL2628 / Plasmid: p15TV-LIC / 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.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1591 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 7.3 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME against PACT Suite A5/5 (0.1 M SPG, pH 8.0, 25% w/v PEG1500), 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: Apr 17, 2014 / 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: 1.9→30 Å / Num. all: 155391 / Num. obs: 155391 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 17.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.4 / Num. unique all: 7680 / % possible all: 97.9

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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 4NI4

4ni4
PDB Unreleased entry


Resolution: 1.9→29.5 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.807 / SU ML: 0.122 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 7795 5 %RANDOM
Rwork0.1936 ---
obs0.1951 147596 98.73 %-
all-147596 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.801 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å2-0.1 Å2
2---2.58 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15456 0 20 1591 17067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916471
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215604
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.95722377
X-RAY DIFFRACTIONr_angle_other_deg1.108336085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4752129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99125.503776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.525152894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1191575
X-RAY DIFFRACTIONr_chiral_restr0.0960.22453
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219233
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023652
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A318890.07
12B318890.07
21A315840.08
22C315840.08
31A318130.07
32D318130.07
41B313060.08
42C313060.08
51B315990.07
52D315990.07
61C316220.07
62D316220.07
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 560 -
Rwork0.258 10678 -
obs-10678 97.01 %
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)
10.52450.0048-0.00851.48840.62711.04750.01430.1127-0.0517-0.0881-0.08840.17220.0124-0.20050.0740.0266-0.0112-0.03270.2743-0.03450.0529100.3007-141.5114188.611
20.56860.46740.00951.190.19340.33880.00630.1076-0.0075-0.1984-0.06020.0679-0.0248-0.13090.05390.08830.032-0.03720.2452-0.00340.0276108.5801-130.9396187.145
30.8723-0.07140.02270.99410.19690.54560.0150.0472-0.0181-0.2061-0.0219-0.02720.0697-0.0260.00690.0868-0.00310.02180.17420.00390.0107127.049-157.6793182.405
40.3069-0.3997-0.0531.47880.07820.3139-0.0154-0.00820.052-0.08190.0253-0.2041-0.02890.0436-0.00990.0241-0.0060.01010.1981-0.00290.0286126.3624-131.4175195.1127
50.19160.1032-0.02242.06690.00260.64070.01360.05380.0096-0.44430.0919-0.4323-0.20920.1815-0.10550.1877-0.07130.15520.2637-0.0060.147140.6104-108.2845188.028
60.3530.2479-0.10941.44920.46040.53450.03270.06650.0268-0.45440.0566-0.1969-0.21390.0893-0.08930.1862-0.01480.09530.24540.00070.0772132.5662-118.4383186.3208
71.38120.2052-0.23151.5763-0.0040.3223-0.04820.12930.1034-0.58850.0370.0791-0.16780.01340.01130.3599-0.0058-0.05060.17730.02910.0168114.0245-91.7833182.6665
80.205-0.2918-0.08351.65760.38560.3172-0.0036-0.0039-0.0107-0.2548-0.00270.1326-0.0751-0.02630.00630.0649-0.0036-0.02240.17520.01510.015114.634-117.804195.2897
90.73580.03990.35150.67670.09930.5786-0.01630.0365-0.01070.13060.0239-0.2657-0.09430.1001-0.00760.0684-0.0212-0.07580.1792-0.00130.1239142.0844-109.1255227.4046
100.57710.17980.13670.75950.11520.3695-0.0057-0.0123-0.02830.20720.0106-0.1853-0.0310.0507-0.0050.07410.0007-0.05840.1728-0.00110.0493130.4671-114.5583229.4656
110.47090.34610.22881.49110.2140.70560.0890.0317-0.09710.37390.0482-0.57450.13440.1724-0.13710.13260.0447-0.19960.2366-0.04620.3094153.4469-138.2083232.483
120.4396-0.25030.03421.00820.00370.27510.04080.03030.00040.15850.0046-0.1820.07520.0215-0.04540.0703-0.0043-0.05220.1831-0.01090.0462129.6351-134.0618223.6235
130.48380.0957-0.25130.7797-0.39340.5562-0.00050.00630.0070.15890.08950.18920.0309-0.1273-0.0890.0771-0.00870.04550.22290.01840.055199.3259-140.7556228.6702
140.59750.1627-0.10690.76530.04750.24480.001-0.0160.02380.21830.01170.02220.0323-0.0485-0.01270.06760.00550.00510.17860.01570.0031112.7257-134.9745229.4036
150.72410.06950.19413.122-0.3450.2858-0.0504-0.1650.00060.70050.12030.5585-0.1577-0.0771-0.06990.22440.07450.18470.29480.05250.177789.9606-111.1786234.2398
160.5201-0.47820.0041.32910.0480.3151-0.0404-0.00150.04360.21750.04490.0014-0.0697-0.0277-0.00440.06220.00160.00670.18950.00430.0058113.2825-115.7478223.9186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 126
2X-RAY DIFFRACTION2A127 - 257
3X-RAY DIFFRACTION3A258 - 403
4X-RAY DIFFRACTION4A404 - 496
5X-RAY DIFFRACTION5B0 - 129
6X-RAY DIFFRACTION6B130 - 257
7X-RAY DIFFRACTION7B258 - 401
8X-RAY DIFFRACTION8B402 - 496
9X-RAY DIFFRACTION9C1 - 129
10X-RAY DIFFRACTION10C130 - 257
11X-RAY DIFFRACTION11C258 - 381
12X-RAY DIFFRACTION12C382 - 496
13X-RAY DIFFRACTION13D-4 - 125
14X-RAY DIFFRACTION14D126 - 258
15X-RAY DIFFRACTION15D259 - 383
16X-RAY DIFFRACTION16D384 - 496

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