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- PDB-4nea: 1.90 Angstrom resolution crystal structure of betaine aldehyde de... -

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Basic information

Entry
Database: PDB / ID: 4nea
Title1.90 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus in complex with NAD+ and BME-free Cys289
ComponentsBetaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / Rossmann fold / NAD+ / National Institute of Allergy and 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
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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. / Winsor, J. / Dubrovska, I. / 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
DepositionOct 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Nov 15, 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_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_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_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)232,99324
Polymers229,7144
Non-polymers3,27920
Water35,8321989
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29810 Å2
ΔGint-101 kcal/mol
Surface area60390 Å2
MethodPISA
2
A: Betaine aldehyde dehydrogenase
C: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,49712
Polymers114,8572
Non-polymers1,64010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-49 kcal/mol
Surface area32950 Å2
MethodPISA
3
B: Betaine aldehyde dehydrogenase
D: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,49712
Polymers114,8572
Non-polymers1,64010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-46 kcal/mol
Surface area33040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.728, 142.073, 163.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Betaine aldehyde dehydrogenase / betB


Mass: 57428.457 Da / Num. of mol.: 4
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 39.098 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1989 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 7 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, 2 mM NAD+, crystallization condition: JCSG+ Suite #G9 (0.1 M potassium thiocyonate, 30% w/v PEG2000 MME), ...Details: 7 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, 2 mM NAD+, crystallization condition: JCSG+ Suite #G9 (0.1 M potassium thiocyonate, 30% w/v PEG2000 MME), 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: Oct 14, 2013 / 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: 1.9→30 Å / Num. all: 155760 / Num. obs: 155760 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 22.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.6 / Num. unique all: 7884 / % possible all: 100

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Processing

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

4mpb


Resolution: 1.9→29.85 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.309 / SU ML: 0.083 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 7781 5 %RANDOM
Rwork0.13965 ---
obs0.14204 147576 97.85 %-
all-147576 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.568 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2--1.27 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15543 0 192 1989 17724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01917270
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216265
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9823561
X-RAY DIFFRACTIONr_angle_other_deg0.85337670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32752218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95125.506781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.349153034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6051577
X-RAY DIFFRACTIONr_chiral_restr0.10.22578
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220073
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023844
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 584 -
Rwork0.192 10983 -
obs-7781 99.89 %
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)
12.77020.6686-0.65398.1609-3.495.6303-0.00330.1184-0.294-0.36990.0096-0.0311-0.04160.1329-0.00640.13870.0102-0.01440.0967-0.06630.06335.4963-14.3079-51.8361
20.6578-0.1765-0.20260.57750.0640.40990.04150.10720.0144-0.0798-0.0358-0.0633-0.0457-0.0127-0.00580.04480.01010.00330.0422-0.00080.00847.33663.9888-49.2799
30.3752-0.11-0.0990.39640.23910.50440.0110.02960.0288-0.00270.0107-0.07660.00630.0264-0.02170.0317-0.00630.00530.0068-0.00070.01739.49878.3989-37.8017
40.5742-0.1427-0.06050.4884-0.03591.04430.0028-0.005-0.08030.00640.0431-0.07010.08040.1076-0.0460.04290.0207-0.00540.0203-0.01970.073421.4568-22.078-37.0167
50.7207-0.1370.17020.95070.02550.5143-0.0377-0.0929-0.05220.1040.032-0.01730.0514-0.01010.00580.0310.0086-0.00280.01330.00390.01568.7542-14.1005-23.9786
60.5222-0.26590.02860.95010.48330.8448-0.0368-0.03090.01560.1121-0.12620.1476-0.0017-0.17890.16310.0736-0.00550.00140.058-0.02510.067-4.409525.5519-16.8503
70.9604-0.31230.19250.87110.00630.56480.03490.1703-0.0814-0.1445-0.06410.08090.0483-0.11560.02920.0438-0.0084-0.02510.1038-0.04860.0513-38.3749-9.3996-46.9445
81.2433-0.73960.83610.9216-0.5270.8394-0.00420.1192-0.0036-0.0421-0.03360.0052-0.0611-0.02090.03780.02040.0144-0.00970.0633-0.00920.0083-22.57791.7875-44.9113
90.431-0.03590.05090.23110.09260.3844-0.00690.0532-0.08570.0016-0.01370.0621-0.016-0.05970.02050.0191-0.0086-0.00120.03-0.01360.0309-30.8469-6.3179-32.7921
100.7194-0.0586-0.23180.93020.25530.85310.02860.13920.1059-0.0306-0.010.1508-0.1541-0.1934-0.01860.08160.0626-0.00320.07670.03180.0728-43.442223.6519-37.1185
110.4452-0.1487-0.08281.37220.01750.5219-0.0004-0.01430.0770.08610.03390.0187-0.0942-0.0294-0.03350.05560.02170.00020.0127-0.00380.0169-28.306217.9994-24.9435
120.49630.2488-0.46460.84390.01560.5216-0.0498-0.16-0.13290.1646-0.0445-0.15220.10530.16520.09430.10970.0118-0.00010.08510.02410.0821-12.9215-19.7071-9.0384
1313.54215.68971.664220.5355-17.259824.90060.1498-0.76660.23561.17730.18590.7581-1.031-0.3709-0.33570.23450.0583-0.03180.1765-0.03740.088715.175122.288615.2472
140.37110.17820.10640.7930.38960.43350.0016-0.075-0.00720.14560.0145-0.10570.01630.0398-0.01610.07390.0062-0.04040.0444-0.00110.024310.4148.3759-2.4847
150.7649-0.39540.00421.2554-0.02960.1578-0.0151-0.00990.07230.05240.0029-0.2169-0.03860.01490.01220.0675-0.003-0.02190.0487-0.02350.051814.025517.3985-17.7248
160.4240.03530.11210.7767-0.02321.4078-0.0062-0.02630.08450.03620.0039-0.0629-0.19710.11390.00230.1004-0.0172-0.03260.0225-0.02480.066811.234939.6265-11.9036
170.5089-0.11030.03621.14990.20840.3279-0.01580.02110.0523-0.031-0.00730.0167-0.0643-0.0240.02310.0458-0.0006-0.01490.0205-0.00910.0175-0.483125.1642-22.8316
180.3213-0.2011-0.19290.62450.17541.1706-0.0450.0229-0.0637-0.04870.01430.0830.1295-0.0470.03060.0544-0.0083-0.0220.03770.00650.06754.2039-17.5921-30.5717
190.5430.081-0.02810.5828-0.35890.94530.0075-0.1706-0.00080.11080.00490.0199-0.0544-0.0986-0.01230.09030.00670.01830.1046-0.00010.0039-26.34430.04856.5343
200.3248-0.05740.13740.2389-0.2080.6999-0.0072-0.1094-0.02330.05050.01060.0105-0.0189-0.0685-0.00340.06460.01290.01130.05130.00280.0083-26.03443.7725-4.4984
211.0879-0.191-0.0160.862-0.26591.3061-0.0221-0.0667-0.07380.08410.02270.15130.1014-0.1874-0.00060.0449-0.00110.02280.06660.01090.0334-37.9154-2.863-10.8661
220.4615-0.1444-0.23820.57170.29381.3888-0.0003-0.1344-0.2120.06640.01020.00580.361-0.1149-0.00990.1874-0.04730.00090.06630.0810.1316-26.3946-30.568-1.1995
230.5099-0.10350.15370.4359-0.20580.67350.0105-0.013-0.1312-0.0295-0.0047-0.00820.1481-0.0032-0.00580.0658-0.00320.00060.00590.00710.0461-18.2187-19.3167-15.9086
240.99380.28630.07680.44430.37750.3612-0.03620.13380.1069-0.13190.01510.0143-0.1332-0.03040.02110.13810.01190.00080.0783-0.00440.0927-25.26920.4812-32.6593
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-23 - 3
2X-RAY DIFFRACTION2A4 - 129
3X-RAY DIFFRACTION3A130 - 257
4X-RAY DIFFRACTION4A258 - 401
5X-RAY DIFFRACTION5A402 - 472
6X-RAY DIFFRACTION6A473 - 496
7X-RAY DIFFRACTION7B-3 - 66
8X-RAY DIFFRACTION8B67 - 129
9X-RAY DIFFRACTION9B130 - 257
10X-RAY DIFFRACTION10B258 - 401
11X-RAY DIFFRACTION11B402 - 474
12X-RAY DIFFRACTION12B475 - 496
13X-RAY DIFFRACTION13C0 - 5
14X-RAY DIFFRACTION14C6 - 211
15X-RAY DIFFRACTION15C212 - 273
16X-RAY DIFFRACTION16C274 - 401
17X-RAY DIFFRACTION17C402 - 474
18X-RAY DIFFRACTION18C475 - 496
19X-RAY DIFFRACTION19D-5 - 129
20X-RAY DIFFRACTION20D130 - 212
21X-RAY DIFFRACTION21D213 - 257
22X-RAY DIFFRACTION22D258 - 401
23X-RAY DIFFRACTION23D402 - 474
24X-RAY DIFFRACTION24D475 - 496

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