PDB-5ez4: 2.11 Angstrom resolution crystal structure of betaine aldehyde de...

ID or keywords:

Entry

Database: PDB / ID: 5ez4

Title

2.11 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289

Components

Betaine aldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / BETAINE ALDEHYDE DEHYDROGENASE /

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 activity / 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: 2.11 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: 2.11 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M/Y450L double 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.

History

Deposition	Nov 26, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 9, 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 Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ez4.cif.gz	821.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ez4.ent.gz	677.1 KB	Display	PDB format
PDBx/mmJSON format	5ez4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ez/5ez4 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/5ez4	HTTPS FTP

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Related structure data

Related structure data	4mpbS 4mpy 4nea 4nu9 4q92 4qje 4qn2 4qto 4zwl 4zxu 5dib 5eyu S: Starting model for refinement
Similar structure data	4zwl-1 4zwl-2 4q92-d 4nu9-1 4qto-d 4qn2-2 4zxu-1 5dib-d 4qje-d 2j6l-1 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

hetero molecules

233 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	225.026, 102.158, 118.330
Angle α, β, γ (deg.)	90.00, 104.85, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-1015- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	A	A	2 - 495	23 - 516
2	1	GLU	GLU	B	B	2 - 495	23 - 516
1	2	MET	MET	A	A	1 - 495	22 - 516
2	2	MET	MET	C	C	1 - 495	22 - 516
1	3	LEU	LEU	A	A	4 - 495	25 - 516
2	3	LEU	LEU	D	D	4 - 495	25 - 516
1	4	GLU	GLU	B	B	2 - 495	23 - 516
2	4	GLU	GLU	C	C	2 - 495	23 - 516
1	5	LEU	LEU	B	B	4 - 495	25 - 516
2	5	LEU	LEU	D	D	4 - 495	25 - 516
1	6	LEU	LEU	C	C	4 - 495	25 - 516
2	6	LEU	LEU	D	D	4 - 495	25 - 516

NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Betaine aldehyde dehydrogenase / Betaine-aldehyde dehydrogenase Mass: 57176.312 Da / Num. of mol.: 4 / Mutation: P449M, Y450L 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

#1: Protein

Betaine aldehyde dehydrogenase / Betaine-aldehyde dehydrogenase

Mass: 57176.312 Da / Num. of mol.: 4 / Mutation: P449M, Y450L
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, 2019 molecules

#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-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2001 / 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: 2.95 Å³/Da / Density % sol: 58.26 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Potein: 6 mg/ml, 10 mM Tris-HCl, pH 8.3, 500 mM NaCl, 5 mM BME, 5mM NAD+. Crystallization: Classics II D3: 100 mM HEPES, pH 7.0, 30%(v/v) Jeffamine ED-2001. Cryo: crystallization condition

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2015
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.11→30 Å / Num. obs: 154078 / % possible obs: 99.9 % / Redundancy: 3.5 % / B_iso Wilson estimate: 21.3 Å² / R_merge(I) obs: 0.136 / Net I/σ(I): 9.92
Reflection shell	Resolution: 2.11→2.15 Å / Redundancy: 3 % / R_merge(I) obs: 0.496 / Mean I/σ(I) obs: 2.06 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
HKL-2000		data scaling
ARP		model building
PHASER		phasing
Coot		model building
BLU-MAX		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4MPB

4mpb

Resolution: 2.11→29.69 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.952 / SU B: 6.389 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17474	7478	5 %	RANDOM
R_work	0.14113	-	-	-
obs	0.14281	141144	99.87 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 22.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.94 Å²	-0 Å²	-0.52 Å²
2-	-	0.86 Å²	-0 Å²
3-	-	-	-1.46 Å²

Refinement step

Cycle: 1 / Resolution: 2.11→29.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15364	0	305	2001	17670

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	16452
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	15581
X-RAY DIFFRACTION	r_angle_refined_deg	1.545	1.976	22332
X-RAY DIFFRACTION	r_angle_other_deg	1.008	3	36034
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.637	5	2087
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.161	25.544	754
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.355	15	2846
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.825	15	76
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	2471
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	18884
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	3600
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	32050	0.04
1	2	B	32050	0.04
2	1	A	31789	0.06
2	2	C	31789	0.06
3	1	A	31666	0.05
3	2	D	31666	0.05
4	1	B	31923	0.06
4	2	C	31923	0.06
5	1	B	31857	0.05
5	2	D	31857	0.05
6	1	C	31705	0.06
6	2	D	31705	0.06

LS refinement shell

Resolution: 2.11→2.165 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.245	568	-
R_work	0.209	10303	-
obs	-	-	99.82 %

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	8.1433	2.0635	0.317	20.2849	2.8029	6.7979	-0.0287	-0.3318	0.8381	-0.145	-0.0986	-0.0958	-0.9259	0.2316	0.1274	0.1866	0.0318	-0.0044	0.1701	0.0492	0.1559	-69.9277	34.8579	9.0724
2	0.3708	-0.0156	0.0229	0.532	-0.0196	0.3082	0.0008	0.0875	0.0511	-0.03	0.0074	0.0601	-0.0419	-0.0685	-0.0082	0.031	0.0212	0.0124	0.0622	0.0272	0.0249	-67.6524	15.6527	16.3363
3	0.4881	-0.0145	-0.0159	1.3416	-0.7561	2.1106	0.0069	0.0151	0.1181	0.0478	0.1133	0.2137	-0.2063	-0.2766	-0.1202	0.0854	0.075	0.0519	0.1001	0.0223	0.1278	-79.7226	29.8335	42.1149
4	0.2115	-0.0371	-0.1149	0.5619	0.2828	0.5996	-0.0049	-0.01	0.0211	0.0605	0.0239	0.0449	0.0327	-0.0805	-0.0189	0.0197	0.0075	0.018	0.0407	0.0119	0.0224	-68.8347	7.0376	37.6543
5	8.773	-4.493	1.0888	13.9507	3.3174	20.9254	-0.2406	0.2108	-0.5536	0.2508	0.2399	-0.1177	0.7675	0.3557	0.0007	0.1458	-0.0441	0.0484	0.0759	-0.001	0.096	-77.8827	-37.8661	41.8665
6	0.3916	0.1291	0.1231	0.5663	0.0445	0.4974	0.0072	-0.0648	-0.0353	0.0188	0.0171	0.0519	0.1254	-0.1903	-0.0243	0.0669	-0.0594	0.0291	0.0985	0.0094	0.0437	-74.0129	-15.5906	37.2858
7	0.9614	0.4056	-0.5811	1.5167	-0.485	1.8405	0.0279	0.0625	-0.1055	-0.1014	0.0085	0.1356	0.3093	-0.214	-0.0364	0.1488	-0.0778	-0.014	0.0781	-0.037	0.0679	-71.8481	-29.6173	9.1479
8	0.2119	-0.0897	0.0037	0.4626	0.2334	0.6548	0.0345	0.0473	-0.0205	-0.0756	-0.0196	-0.0026	0.0569	-0.0547	-0.015	0.0438	-0.0144	0.0095	0.0549	0.0006	0.0229	-64.4882	-7.8167	17.2327
9	15.1932	-13.542	-13.3992	12.0866	11.9501	11.8219	-0.7021	0.2724	-1.0172	0.7485	-0.233	0.9652	0.6917	-0.2855	0.9351	0.79	-0.2296	0.1599	0.848	0.173	0.682	-37.2781	-30.9845	66.2623
10	0.5307	-0.0229	0.2673	0.1618	-0.0828	0.5342	0.0732	-0.0557	-0.1245	0.0306	-0.001	-0.0438	0.0796	0.0305	-0.0722	0.0323	0.0019	-0.025	0.0211	0.0073	0.0579	-34.0835	-17.4469	46.2673
11	0.938	-0.0475	0.2582	1.5283	-0.046	0.5396	-0.0859	-0.2889	-0.0135	0.2492	0.0734	-0.0944	-0.0418	-0.1089	0.0125	0.0828	0.0544	-0.0262	0.1646	-0.0142	0.0159	-35.7366	1.1861	72.0288
12	0.3768	-0.0312	0.0348	0.3044	0.0788	0.8612	-0.0358	-0.0636	0.0578	0.0473	0.0212	-0.0349	-0.0334	-0.0496	0.0147	0.0129	0.0114	-0.0165	0.0255	-0.0074	0.0554	-38.5388	5.5678	46.9872
13	1.0461	0.0399	-0.1377	0.5415	0.2026	0.9892	0.001	0.0898	0.133	-0.0339	0.0101	-0.094	-0.1715	0.0961	-0.0111	0.0537	-0.0274	0.0101	0.0328	0.0344	0.0986	-27.8373	21.3539	24.0374
14	0.3735	0.0409	0.0028	0.4075	-0.1139	0.5622	0.0035	0.038	0.0949	0.0035	-0.0082	-0.0612	-0.0517	0.067	0.0047	0.0092	-0.0107	-0.0027	0.029	0.0061	0.0492	-29.1674	12.1132	33.1053
15	0.8029	0.0918	-0.0006	1.8256	0.0423	0.6974	0.0285	0.1991	0.0052	-0.1149	0.0276	-0.2815	-0.0543	0.1682	-0.0562	0.0357	-0.0253	0.0575	0.1728	-0.0366	0.1014	-17.2995	-2.3278	5.7351
16	0.4713	-0.1142	-0.0166	0.2925	0.1523	0.665	0.0036	0.0648	-0.0453	-0.0105	0.0365	-0.0447	0.0586	0.0383	-0.0401	0.0077	-0.0014	-0.0029	0.0364	-0.009	0.0609	-32.79	-6.3908	25.583

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 10
2	X-RAY DIFFRACTION	2	A	11 - 258
3	X-RAY DIFFRACTION	3	A	259 - 381
4	X-RAY DIFFRACTION	4	A	382 - 496
5	X-RAY DIFFRACTION	5	B	2 - 6
6	X-RAY DIFFRACTION	6	B	7 - 258
7	X-RAY DIFFRACTION	7	B	259 - 374
8	X-RAY DIFFRACTION	8	B	375 - 496
9	X-RAY DIFFRACTION	9	C	-1 - 6
10	X-RAY DIFFRACTION	10	C	7 - 258
11	X-RAY DIFFRACTION	11	C	259 - 379
12	X-RAY DIFFRACTION	12	C	380 - 496
13	X-RAY DIFFRACTION	13	D	4 - 126
14	X-RAY DIFFRACTION	14	D	127 - 257
15	X-RAY DIFFRACTION	15	D	258 - 379
16	X-RAY DIFFRACTION	16	D	380 - 496

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 2019 molecules

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Experimental details

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Sample preparation

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Data collection

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About Yorodumi

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Yorodumi