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- PDB-4qto: 1.65 Angstrom resolution crystal structure of betaine aldehyde de... -

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Basic information

Entry
Database: PDB / ID: 4qto
Title1.65 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus with BME-modified Cys289 and PEG molecule in active site
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


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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Betaine aldehyde dehydrogenase / Betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / 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
DepositionJul 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 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_asym_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_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_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.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

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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)231,99823
Polymers230,0184
Non-polymers1,98019
Water47,9742663
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25540 Å2
ΔGint-70 kcal/mol
Surface area61280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.249, 102.474, 118.178
Angle α, β, γ (deg.)90.00, 104.45, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYSAA0 - 49624 - 520
21ALAALALYSLYSBB0 - 49624 - 520
12METMETSERSERAA1 - 49525 - 519
22METMETSERSERCC1 - 49525 - 519
13GLUGLUSERSERAA2 - 49526 - 519
23GLUGLUSERSERDD2 - 49526 - 519
14METMETSERSERBB1 - 49525 - 519
24METMETSERSERCC1 - 49525 - 519
15GLUGLUSERSERBB2 - 49526 - 519
25GLUGLUSERSERDD2 - 49526 - 519
16GLUGLUSERSERCC2 - 49526 - 519
26GLUGLUSERSERDD2 - 49526 - 519

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Betaine aldehyde dehydrogenase


Mass: 57504.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Gene: betB, SACOL2628 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Magic
References: UniProt: Q5HCU0, UniProt: A0A0H2X0S3*PLUS, betaine-aldehyde dehydrogenase

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Non-polymers , 7 types, 2682 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2663 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 7 mg/mL protein in 10 mM betaine (not observed in structure), 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME, crystallization: The Classics II Suite D4 (40): 0.1 M citric acid, pH ...Details: 7 mg/mL protein in 10 mM betaine (not observed in structure), 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME, crystallization: The Classics II Suite D4 (40): 0.1 M citric acid, pH 3.5, 25% w/v PEG3350, cryoprotectant: well solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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: Jun 16, 2014 / Details: beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 307248 / Num. obs: 307248 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.5 / Num. unique all: 15078 / % possible all: 97.5

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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: 1.65→29.71 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.421 / SU ML: 0.042 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15554 15433 5 %RANDOM
Rwork0.1359 ---
obs0.13689 290362 98.57 %-
all-290362 --
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: 18.754 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å2-0.34 Å2
2---0.05 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15398 0 129 2663 18190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01917047
X-RAY DIFFRACTIONr_bond_other_d0.0060.0216260
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.96223184
X-RAY DIFFRACTIONr_angle_other_deg1.14337659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.08452237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81125.591787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.897152996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0541577
X-RAY DIFFRACTIONr_chiral_restr0.110.22533
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220029
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023764
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A325790.06
12B325790.06
21A319190.07
22C319190.07
31A318230.07
32D318230.07
41B316740.07
42C316740.07
51B315810.07
52D315810.07
61C315230.08
62D315230.08
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 1168 -
Rwork0.21 21045 -
obs-21045 97.49 %
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)
10.6012-1.25460.047910.92461.80846.34820.0340.18340.22280.1463-0.0597-0.4066-0.71410.05190.02570.12760.02010.00250.06940.07310.0954266.844886.60989.7491
20.4617-0.11330.15670.4484-0.06370.5048-0.01130.06340.0446-0.0230.0142-0.0035-0.0844-0.0268-0.00290.02190.0160.01010.03930.02680.0193270.743272.720814.949
30.2073-0.03580.04540.4915-0.10430.23490.0050.06680.0282-0.0088-0.00380.0333-0.034-0.0414-0.00120.0070.011400.03670.00880.0093267.311461.824817.7846
40.43690.0727-0.16180.4625-0.05531.18070.03330.02680.0886-0.0155-0.02390.0839-0.1716-0.1581-0.00940.0540.05350.0020.0562-0.01020.0656257.322581.671342.1137
50.1022-0.0538-0.06810.42440.38780.56520.0013-0.00370.00450.0297-0.01620.01550.0176-0.06840.01490.0060.00620.00660.0294-0.00090.0227267.5558.857838.012
64.7243-0.8737-3.075316.92366.22893.9327-0.45980.0824-0.64510.23810.2853-0.7450.41370.0030.17450.2251-0.11230.08420.1411-0.00540.2166257.911315.485841.0167
70.48550.16560.03320.4384-0.02350.5564-0.0003-0.0353-0.03080.0330.01760.01910.1442-0.1172-0.01730.053-0.04570.00220.06310.0120.0295263.268130.501739.3459
80.19630.11010.06250.4614-0.01810.32870.0221-0.0389-0.0102-0.0273-0.00840.02630.0655-0.1092-0.01370.0205-0.02310.00620.05060.00040.0327262.267941.549535.213
90.45920.0682-0.21760.6677-0.24861.2640.05150.0643-0.0857-0.0674-0.01230.07880.2421-0.1447-0.03920.0919-0.0436-0.0120.0526-0.03070.0464264.552522.04718.6797
100.1164-0.0631-0.02880.34220.29170.49570.01560.0445-0.0021-0.0585-0.0099-0.0258-0.0058-0.0318-0.00570.0179-0.00190.00690.0263-0.00520.0065272.68144.569218.1385
119.36190.2274-2.275622.12835.464117.2065-0.1925-0.5754-0.12171.43610.15991.05290.751-0.65930.03260.1347-0.00510.0260.10860.0710.1454299.92820.263363.6347
120.5097-0.09170.26740.1319-0.13940.5350.0801-0.0395-0.1381-0.0219-0.0067-0.00830.0661-0.0025-0.07340.0186-0.0035-0.03210.0090.00770.0786300.485629.85749.8514
130.33330.02250.13420.2079-0.26450.49290.0493-0.0018-0.08050.0116-0.0067-0.02440.00690.022-0.04260.01480.0099-0.01660.0189-0.01250.0562304.839138.157642.4577
140.5531-0.09930.34180.8606-0.18280.4738-0.0895-0.20260.00780.16990.0484-0.0693-0.0935-0.10180.04110.04760.0405-0.02280.0899-0.01450.0223301.927553.835771.0332
150.2555-0.08190.05210.11540.07910.5865-0.0375-0.00990.03670.00340.0314-0.0161-0.0549-0.00230.00610.0109-0.0001-0.01040.0152-0.00530.0379296.288556.327242.7547
165.26380.90840.69385.7437-0.027215.24410.0690.50420.4399-0.63480.1463-0.0759-0.63290.2046-0.21530.161-0.05510.02120.10450.08350.1397316.096182.099516.9026
170.61640.0503-0.05840.38160.090.6161-0.00910.07320.0987-0.0250.0048-0.0542-0.12290.07120.00430.0288-0.0221-0.00170.0310.02540.0673308.07371.771224.4658
180.35280.0659-0.05660.2584-0.13110.4522-0.01260.04640.0551-0.00190.0014-0.0398-0.02640.05030.01110.0104-0.0124-0.00880.0292-0.00010.0474307.96963.556332.8428
190.37210.104-0.07981.348-0.04930.6344-0.02180.1673-0.0527-0.08450.0666-0.2482-0.02440.1755-0.04480.0099-0.02080.0280.1484-0.04580.0815319.679847.86.6838
200.371-0.0625-0.08560.08560.08260.4963-0.01120.0289-0.04610.00930.03110.00130.050.0329-0.01980.00620.0048-0.00490.0214-0.01110.0332300.118645.807628.0252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 10
2X-RAY DIFFRACTION2A11 - 129
3X-RAY DIFFRACTION3A130 - 258
4X-RAY DIFFRACTION4A259 - 378
5X-RAY DIFFRACTION5A379 - 496
6X-RAY DIFFRACTION6B0 - 9
7X-RAY DIFFRACTION7B10 - 129
8X-RAY DIFFRACTION8B130 - 258
9X-RAY DIFFRACTION9B259 - 381
10X-RAY DIFFRACTION10B382 - 496
11X-RAY DIFFRACTION11C1 - 7
12X-RAY DIFFRACTION12C8 - 129
13X-RAY DIFFRACTION13C130 - 257
14X-RAY DIFFRACTION14C258 - 401
15X-RAY DIFFRACTION15C402 - 496
16X-RAY DIFFRACTION16D2 - 10
17X-RAY DIFFRACTION17D11 - 129
18X-RAY DIFFRACTION18D130 - 258
19X-RAY DIFFRACTION19D259 - 401
20X-RAY DIFFRACTION20D402 - 496

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