PDB-4zxu: 2.85 Angstrom resolution crystal structure of betaine aldehyde de...

ID or keywords:

Entry

Database: PDB / ID: 4zxu

Title

2.85 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) H448F/P449M double mutant from Staphylococcus aureus in complex with NAD+ and BME-free Cys289

Components

Betaine-aldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / betaine aldehyde dehydrogenase / 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

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Halavaty, 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: 2.85 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) H448F/P449M double mutant from Staphylococcus aureus in complex with NAD+ and BME-free Cys289.
Authors: Halavaty, A.S. / Minasov, G. / Chen, C. / Joo, J.C. / Yakunin, A.F. / Anderson, W.F.

History

Deposition	May 20, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4zxu_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	4zxu_full_validation.pdf.gz	2.7 MB	Display
Data in XML	4zxu_validation.xml.gz	134.8 KB	Display
Data in CIF	4zxu_validation.cif.gz	184 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zx/4zxu ftp://data.pdbj.org/pub/pdb/validation_reports/zx/4zxu	HTTPS FTP

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Related structure data

Related structure data	4mpbS 4mpy 4nea 4nu9 4q92 4qje 4qn2 4qto 4zwl S: Starting model for refinement
Similar structure data	4qto-d 5dib-d 4qn2-2 4zwl-1 4zwl-2 4qn2-1 4mpb-3 4mpy-2 5ez4-d 4q92-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP00699

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: Betaine-aldehyde dehydrogenase

B: Betaine-aldehyde dehydrogenase

C: Betaine-aldehyde dehydrogenase

D: Betaine-aldehyde dehydrogenase

E: Betaine-aldehyde dehydrogenase

F: Betaine-aldehyde dehydrogenase

G: Betaine-aldehyde dehydrogenase

H: Betaine-aldehyde dehydrogenase

hetero molecules

464 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Betaine-aldehyde dehydrogenase

B: Betaine-aldehyde dehydrogenase

C: Betaine-aldehyde dehydrogenase

D: Betaine-aldehyde dehydrogenase

hetero molecules

defined by author&software
232 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Betaine-aldehyde dehydrogenase

F: Betaine-aldehyde dehydrogenase

G: Betaine-aldehyde dehydrogenase

H: Betaine-aldehyde dehydrogenase

hetero molecules

defined by author&software
232 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	88.998, 168.999, 144.467
Angle α, β, γ (deg.)	90.00, 104.51, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	SER	SER	A	A	0 - 495	21 - 516
2	1	GLY	GLY	SER	SER	B	B	0 - 495	21 - 516
1	2	MET	MET	SER	SER	A	A	1 - 495	22 - 516
2	2	MET	MET	SER	SER	C	C	1 - 495	22 - 516
1	3	MET	MET	SER	SER	A	A	1 - 495	22 - 516
2	3	MET	MET	SER	SER	D	D	1 - 495	22 - 516
1	4	GLN	GLN	SER	SER	A	A	-1 - 495	20 - 516
2	4	GLN	GLN	SER	SER	E	E	-1 - 495	20 - 516
1	5	GLU	GLU	SER	SER	A	A	2 - 495	23 - 516
2	5	GLU	GLU	SER	SER	F	F	2 - 495	23 - 516
1	6	GLY	GLY	SER	SER	A	A	0 - 495	21 - 516
2	6	GLY	GLY	SER	SER	G	G	0 - 495	21 - 516
1	7	MET	MET	SER	SER	A	A	1 - 495	22 - 516
2	7	MET	MET	SER	SER	H	H	1 - 495	22 - 516
1	8	MET	MET	SER	SER	B	B	1 - 495	22 - 516
2	8	MET	MET	SER	SER	C	C	1 - 495	22 - 516
1	9	MET	MET	SER	SER	B	B	1 - 495	22 - 516
2	9	MET	MET	SER	SER	D	D	1 - 495	22 - 516
1	10	GLY	GLY	SER	SER	B	B	0 - 495	21 - 516
2	10	GLY	GLY	SER	SER	E	E	0 - 495	21 - 516
1	11	GLU	GLU	SER	SER	B	B	2 - 495	23 - 516
2	11	GLU	GLU	SER	SER	F	F	2 - 495	23 - 516
1	12	GLY	GLY	LYS	LYS	B	B	0 - 496	21 - 517
2	12	GLY	GLY	LYS	LYS	G	G	0 - 496	21 - 517
1	13	MET	MET	SER	SER	B	B	1 - 495	22 - 516
2	13	MET	MET	SER	SER	H	H	1 - 495	22 - 516
1	14	MET	MET	LYS	LYS	C	C	1 - 496	22 - 517
2	14	MET	MET	LYS	LYS	D	D	1 - 496	22 - 517
1	15	MET	MET	SER	SER	C	C	1 - 495	22 - 516
2	15	MET	MET	SER	SER	E	E	1 - 495	22 - 516
1	16	GLU	GLU	SER	SER	C	C	2 - 495	23 - 516
2	16	GLU	GLU	SER	SER	F	F	2 - 495	23 - 516
1	17	MET	MET	SER	SER	C	C	1 - 495	22 - 516
2	17	MET	MET	SER	SER	G	G	1 - 495	22 - 516
1	18	MET	MET	LYS	LYS	C	C	1 - 496	22 - 517
2	18	MET	MET	LYS	LYS	H	H	1 - 496	22 - 517
1	19	MET	MET	SER	SER	D	D	1 - 495	22 - 516
2	19	MET	MET	SER	SER	E	E	1 - 495	22 - 516
1	20	GLU	GLU	SER	SER	D	D	2 - 495	23 - 516
2	20	GLU	GLU	SER	SER	F	F	2 - 495	23 - 516
1	21	MET	MET	SER	SER	D	D	1 - 495	22 - 516
2	21	MET	MET	SER	SER	G	G	1 - 495	22 - 516
1	22	MET	MET	LYS	LYS	D	D	1 - 496	22 - 517
2	22	MET	MET	LYS	LYS	H	H	1 - 496	22 - 517
1	23	GLU	GLU	SER	SER	E	E	2 - 495	23 - 516
2	23	GLU	GLU	SER	SER	F	F	2 - 495	23 - 516
1	24	GLY	GLY	SER	SER	E	E	0 - 495	21 - 516
2	24	GLY	GLY	SER	SER	G	G	0 - 495	21 - 516
1	25	MET	MET	SER	SER	E	E	1 - 495	22 - 516
2	25	MET	MET	SER	SER	H	H	1 - 495	22 - 516
1	26	GLU	GLU	SER	SER	F	F	2 - 495	23 - 516
2	26	GLU	GLU	SER	SER	G	G	2 - 495	23 - 516
1	27	GLU	GLU	SER	SER	F	F	2 - 495	23 - 516
2	27	GLU	GLU	SER	SER	H	H	2 - 495	23 - 516
1	28	MET	MET	SER	SER	G	G	1 - 495	22 - 516
2	28	MET	MET	SER	SER	H	H	1 - 495	22 - 516

NCS ensembles :

#1: Protein	Betaine-aldehyde dehydrogenase Mass: 57159.234 Da / Num. of mol.: 8 / Mutation: H448F, P449M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: betB, SACOL2628 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMAGIC References: UniProt: Q5HCU0, UniProt: A0A0M3KL41*PLUS, betaine-aldehyde dehydrogenase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.52 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Crystallization: The Classics II Suite G5: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350. Protein: 5 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 0.5 mM TCEP, 5 mM NAD+. Cryo: ...Details: Crystallization: The Classics II Suite G5: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350. Protein: 5 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 0.5 mM TCEP, 5 mM NAD+. Cryo: crystallization condition

Crystal

Density Matthews: 2.3 Å³/Da / Density % sol: 46.52 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization: The Classics II Suite G5: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350. Protein: 5 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 0.5 mM TCEP, 5 mM NAD+. Cryo: ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2014
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.85→30 Å / Num. obs: 96507 / % possible obs: 100 % / Redundancy: 3.8 % / B_iso Wilson estimate: 64.4 Å² / R_merge(I) obs: 0.117 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.85→2.9 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.683 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4mpb

4mpb

Resolution: 2.85→29.89 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.931 / SU B: 29.38 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21253	4864	5.1 %	RANDOM
R_work	0.16422	-	-	-
obs	0.16666	91344	99.85 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 55.333 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.53 Å²	-0 Å²	-0.06 Å²
2-	-	-0.51 Å²	-0 Å²
3-	-	-	2.7 Å²

Refinement step

Cycle: 1 / Resolution: 2.85→29.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30833	0	427	420	31680

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	32563
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	30742
X-RAY DIFFRACTION	r_angle_refined_deg	1.615	1.973	44216
X-RAY DIFFRACTION	r_angle_other_deg	1.098	3	71057
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.156	5	4126
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.35	25.493	1491
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.095	15	5702
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.31	15	147
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	4899
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	37348
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	7119
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	31757	0.05
1	2	B	31757	0.05
2	1	A	31588	0.05
2	2	C	31588	0.05
3	1	A	31645	0.05
3	2	D	31645	0.05
4	1	A	31741	0.05
4	2	E	31741	0.05
5	1	A	31652	0.05
5	2	F	31652	0.05
6	1	A	31710	0.05
6	2	G	31710	0.05
7	1	A	31652	0.05
7	2	H	31652	0.05
8	1	B	31656	0.05
8	2	C	31656	0.05
9	1	B	31727	0.04
9	2	D	31727	0.04
10	1	B	31701	0.04
10	2	E	31701	0.04
11	1	B	31722	0.04
11	2	F	31722	0.04
12	1	B	31758	0.04
12	2	G	31758	0.04
13	1	B	31746	0.04
13	2	H	31746	0.04
14	1	C	31739	0.05
14	2	D	31739	0.05
15	1	C	31726	0.05
15	2	E	31726	0.05
16	1	C	31627	0.05
16	2	F	31627	0.05
17	1	C	31643	0.05
17	2	G	31643	0.05
18	1	C	31859	0.05
18	2	H	31859	0.05
19	1	D	31637	0.04
19	2	E	31637	0.04
20	1	D	31677	0.04
20	2	F	31677	0.04
21	1	D	31656	0.05
21	2	G	31656	0.05
22	1	D	31837	0.05
22	2	H	31837	0.05
23	1	E	31590	0.04
23	2	F	31590	0.04
24	1	E	31747	0.04
24	2	G	31747	0.04
25	1	E	31699	0.04
25	2	H	31699	0.04
26	1	F	31668	0.04
26	2	G	31668	0.04
27	1	F	31704	0.05
27	2	H	31704	0.05
28	1	G	31705	0.05
28	2	H	31705	0.05

LS refinement shell

Resolution: 2.85→2.923 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.32	364	-
R_work	0.257	6651	-
obs	-	-	99.73 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.7041	0.024	-0.0401	0.3983	-0.0741	0.4851	0.0184	0.0248	0.123	-0.0229	-0.011	-0.0326	-0.1152	0.0249	-0.0073	0.0653	-0.0038	0.0203	0.0298	-0.0038	0.0333	1.7217	-9.1044	-8.7937
2	0.7964	-0.1083	0.0197	0.5258	-0.0256	0.5489	-0.0288	-0.2108	-0.109	0.0413	0.0014	-0.031	0.1644	0.0746	0.0274	0.0789	0.0109	0.0288	0.083	0.0202	0.0364	5.6624	-38.1631	11.639
3	0.6545	-0.055	0.2243	0.3427	-0.0275	0.5314	0.0339	0.0685	-0.2326	-0.0829	0.0229	0.0021	0.1552	-0.0285	-0.0568	0.1197	-0.0584	0.0285	0.0433	-0.0494	0.1005	-28.3908	-49.0226	-17.2688
4	0.6299	-0.024	0.2545	0.2939	-0.0349	0.3322	-0.0362	-0.1848	0.0244	0.0418	0.0596	0.0262	-0.0164	-0.189	-0.0234	0.0546	-0.0087	0.0371	0.1476	-0.0112	0.0348	-41.0934	-21.8376	1.6193
5	0.8259	-0.1223	0.02	0.5571	0.0087	0.2297	-0.0544	-0.1162	-0.1342	0.0467	0.0451	0.1318	0.0274	-0.0477	0.0094	0.0672	0.0468	0.0301	0.1054	0.0245	0.049	-0.503	3.0546	-63.0884
6	0.7089	0.1306	-0.044	0.5527	-0.0248	0.305	-0.0051	-0.1908	0.1273	0.0911	-0.0085	-0.1217	-0.0372	0.067	0.0137	0.0737	0.0592	-0.0257	0.1608	-0.0273	0.0661	42.5307	16.0896	-54.0208
7	0.5672	-0.2627	0.1119	0.8005	0.1641	0.4321	-0.0029	0.0093	-0.0618	-0.0445	0.0166	-0.1593	0.1326	0.1119	-0.0136	0.0895	0.0658	0.053	0.1279	0.0228	0.0785	46.1073	-11.2166	-76.3696
8	0.7103	-0.2369	0.0115	0.575	-0.1692	0.4794	0.0442	0.1903	0.0465	-0.1948	-0.0572	-0.0465	0.0328	0.0167	0.013	0.1374	0.0342	0.0145	0.1311	0.0156	0.0052	12.2163	14.0189	-94.4123

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-4 - 496
2	X-RAY DIFFRACTION	2	B	0 - 496
3	X-RAY DIFFRACTION	3	C	1 - 496
4	X-RAY DIFFRACTION	4	D	1 - 496
5	X-RAY DIFFRACTION	5	E	-1 - 496
6	X-RAY DIFFRACTION	6	F	2 - 496
7	X-RAY DIFFRACTION	7	G	0 - 496
8	X-RAY DIFFRACTION	8	H	1 - 496

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