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- PDB-5eyu: 1.72 Angstrom resolution crystal structure of betaine aldehyde de... -

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Basic information

Entry
Database: PDB / ID: 5eyu
Title1.72 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M point mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289
ComponentsBetaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / BetB / ROSSMANN FOLD / STRUCTURAL GENOMICS / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


cellular response to chemical stimulus / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase (NAD+) 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 / TRIETHYLENE GLYCOL / Betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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: 1.72 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M point mutant from Staphylococcus aureus in complex with NAD+ and BME-modified 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.
#2: 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.
History
DepositionNov 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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_conn_type / struct_ncs_dom_lim
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.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.conn_type_id / _struct_conn.id / _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_conn_type.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

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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)233,29724
Polymers228,9054
Non-polymers4,39220
Water42,0472334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28910 Å2
ΔGint-165 kcal/mol
Surface area59480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.271, 102.721, 117.810
Angle α, β, γ (deg.)90.00, 104.75, 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: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 6 - 496 / Label seq-ID: 27 - 517

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

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 / Betaine-aldehyde dehydrogenase


Mass: 57226.328 Da / Num. of mol.: 4 / Mutation: P449M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PMAGIC / References: UniProt: Q9L4P8, betaine-aldehyde dehydrogenase

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Non-polymers , 5 types, 2354 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2334 / 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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 7 mg/ml in 10 mM Tris-HCl, pH 8.3, 500 mM NaCl, 5 mM BME, 5 mM NAD. Crystallization: The Classics II Suite D3: 100 mM HEPES, pH 7.0, 30%(v/v) Jeffamine ED-2001. Cryo: crystallization condition

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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: Jun 29, 2015
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. obs: 271627 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.3
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.05 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
BLU-MAXdata collection
Cootmodel building
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MPB

4mpb


Resolution: 1.72→29.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.291 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18295 13698 5.1 %RANDOM
Rwork0.16373 ---
obs0.1647 257471 99.15 %-
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: 17.824 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20.07 Å2
2--1.37 Å20 Å2
3----1.64 Å2
Refinement stepCycle: 1 / Resolution: 1.72→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15232 0 284 2334 17850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916409
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215524
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.97522285
X-RAY DIFFRACTIONr_angle_other_deg0.97335910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.69652084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40725.469746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.811152838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7821575
X-RAY DIFFRACTIONr_chiral_restr0.0890.22459
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218839
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023596
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
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A321670.05
12B321670.05
21A318590.07
22C318590.07
31A318170.07
32D318170.07
41B316610.06
42C316610.06
51B316880.06
52D316880.06
61C316030.07
62D316030.07
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 877 -
Rwork0.269 17182 -
obs--89.89 %
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)
10.559-0.19330.06290.63930.02750.5598-0.00340.07470.0597-0.04080.01420.028-0.0724-0.0566-0.01080.05230.0157-0.01620.03670.03470.0644-66.005321.826214.1731
20.2664-0.01490.03270.5352-0.13380.31480.01170.0610.0253-0.0032-0.00440.045-0.0133-0.0928-0.00730.04450.0101-0.0310.0510.00830.0626-68.72449.901217.6122
30.42760.043-0.09950.9099-0.41041.32320.0260.03340.07870.06740.04340.2-0.1496-0.1973-0.06940.0840.05770.00840.04950.00690.1312-79.94128.506541.8986
40.4485-0.1313-0.27620.72290.38631.6604-0.0207-0.03630.01640.1199-0.00490.05540.0253-0.07760.02560.04990.0111-0.01320.01540.00040.0669-69.095412.830344.4766
50.2960.1872-0.08261.15920.32820.6624-0.03490.0011-0.06720.05180.0681-0.15370.18320.0263-0.03320.0832-0.0046-0.030.0158-0.00720.0642-57.4331-15.367218.1129
60.66630.17220.09330.7210.10580.9678-0.0088-0.0387-0.05960.02040.02430.04820.1587-0.1892-0.01550.0798-0.0651-0.02390.06520.02560.0612-73.7583-21.876839.4669
70.26990.090.02140.5091-0.04270.41580.0064-0.0205-0.0175-0.01270.00630.05860.0723-0.1505-0.01260.0389-0.034-0.01780.05830.00270.0652-73.8966-9.929935.174
80.66030.1425-0.42750.7756-0.35981.76510.00110.0893-0.0801-0.12470.02730.11070.3123-0.2499-0.02850.1606-0.0783-0.04020.0702-0.03060.1067-71.8606-29.6378.7375
90.4781-0.02830.11470.48720.22961.0670.01880.0784-0.0326-0.1109-0.0020.00220.0628-0.0833-0.01680.0797-0.0209-0.02080.0293-0.00950.0613-64.0811-14.515210.5391
100.2252-0.249-0.07381.4810.01460.5417-0.02550.01020.05520.0520.0727-0.1214-0.1080.0349-0.04720.0425-0.0048-0.01710.0141-0.00090.0678-62.750814.863140.6955
110.971-0.23250.53850.1685-0.17210.84580.0729-0.0767-0.1998-0.00650.01670.00250.0927-0.0399-0.08960.081-0.0162-0.07190.00880.01660.1585-36.0753-22.118949.8836
120.468-0.04620.20630.2651-0.21640.64540.0387-0.0009-0.09460.00940.016-0.0350.03020.0457-0.05480.04560.0067-0.05720.0094-0.0140.1115-31.759-13.581242.3518
131.0469-0.27910.34761.1692-0.25530.6865-0.1306-0.29520.02930.21620.09-0.0903-0.1234-0.13360.04050.1050.0616-0.06910.1276-0.02480.0786-34.6622.163870.756
140.8795-0.32050.09120.55580.12670.9841-0.0959-0.13990.10390.08650.0736-0.0479-0.0914-0.07980.02230.05550.0261-0.05760.0295-0.01940.0836-41.81818.168653.8732
150.85080.3669-0.68790.5443-0.43261.70080.01860.16870.0442-0.05540.0580.0188-0.0771-0.1617-0.07650.04940.019-0.0430.0394-0.01140.105-36.6982-4.232416.3486
160.8775-0.0651-0.20590.48650.09790.66570.02080.0620.1175-0.0294-0.0026-0.0896-0.13270.0676-0.01820.0646-0.0256-0.02720.01830.01950.1339-27.806820.803924.0494
170.40930.0885-0.05720.4247-0.14840.4831-0.00360.0260.06850.01420.0079-0.0679-0.02950.0504-0.00440.0392-0.0094-0.04460.014-0.00230.102-28.975111.808232.9267
180.57790.0601-0.07011.33890.080.73680.01750.1552-0.0205-0.06510.0218-0.2513-0.01810.1658-0.03930.0463-0.0041-0.00790.1177-0.03570.1448-16.9573-3.86326.8601
190.4759-0.1323-0.1471.00230.42990.88570.00310.0959-0.0759-0.00410.0212-0.03890.10080.0346-0.02430.03120.0055-0.03520.0287-0.02240.0891-31.991-9.802817.4352
200.8932-0.178-0.12170.3695-0.38722.0356-0.0882-0.1609-0.00140.04110.13560.05860.0756-0.2206-0.04740.05980.0255-0.03890.0749-0.00670.1093-46.60533.038852.4645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 126
2X-RAY DIFFRACTION2A127 - 257
3X-RAY DIFFRACTION3A258 - 399
4X-RAY DIFFRACTION4A400 - 469
5X-RAY DIFFRACTION5A470 - 496
6X-RAY DIFFRACTION6B6 - 126
7X-RAY DIFFRACTION7B127 - 258
8X-RAY DIFFRACTION8B259 - 381
9X-RAY DIFFRACTION9B382 - 469
10X-RAY DIFFRACTION10B470 - 496
11X-RAY DIFFRACTION11C6 - 129
12X-RAY DIFFRACTION12C130 - 257
13X-RAY DIFFRACTION13C258 - 402
14X-RAY DIFFRACTION14C403 - 469
15X-RAY DIFFRACTION15C470 - 496
16X-RAY DIFFRACTION16D6 - 126
17X-RAY DIFFRACTION17D127 - 257
18X-RAY DIFFRACTION18D258 - 401
19X-RAY DIFFRACTION19D402 - 469
20X-RAY DIFFRACTION20D470 - 496

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