PDB-3iv3: The Structure of a putative tagatose 1,6-aldolase from Streptococ...

ID or keywords:

Entry

Database: PDB / ID: 3iv3

Title

The Structure of a putative tagatose 1,6-aldolase from Streptococcus mutans

Components

Tagatose 1,6-diphosphate aldolase 2

Keywords

LYASE / TIM barrel / phosphate binding / TAGATOSE-BISPHOSPHATE ALDOLASE / D-TAGATOSE-1 / 6-BISPHOSPHATE ALDOLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Lactose metabolism

Function / homology

Function and homology information

tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / 6-deoxy-6-sulfofructose-1-phosphate aldolase activity / lactose catabolic process via tagatose-6-phosphate / 6-sulfoquinovose(1-) catabolic process / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity
Similarity search - Function

Biological species

Streptococcus mutans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Cuff, M.E. / Hatzos, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The Structure of a putative tagatose 1,6-aldolase from Streptococcus mutans
Authors: Cuff, M.E. / Hatzos, C. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Aug 31, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 22, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3iv3.cif.gz	91.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3iv3.ent.gz	67 KB	Display	PDB format
PDBx/mmJSON format	3iv3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3iv3_validation.pdf.gz	442.9 KB	Display	wwPDB validaton report
Full document	3iv3_full_validation.pdf.gz	443.8 KB	Display
Data in XML	3iv3_validation.xml.gz	20.3 KB	Display
Data in CIF	3iv3_validation.cif.gz	29.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iv/3iv3 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/3iv3	HTTPS FTP

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Related structure data

Similar structure data	6ek1-1 2hsa-d 3amg-d 4f13-d 3wux-2 6b10-d 5or3-1 5or4-1 5or4-2 2zw9-1 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	TargetDB: apc63936

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (3)

Deposited unit

A: Tagatose 1,6-diphosphate aldolase 2

hetero molecules

37.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tagatose 1,6-diphosphate aldolase 2

hetero molecules

A: Tagatose 1,6-diphosphate aldolase 2

hetero molecules

defined by author&software
75.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	104.214, 113.759, 74.399
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Tagatose 1,6-diphosphate aldolase 2 / Tagatose-bisphosphate aldolase 2 / D-tagatose-1 / 6-bisphosphate aldolase 2 Mass: 37193.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: lacD2, SMU_116 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8DWE5, tagatose-bisphosphate aldolase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.51 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.49 M Sodium phosphate monobasic monohydrate, 0.91 M Potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97951, 0.97937

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2009

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97951	1
2	0.97937	1

Reflection

Redundancy: 15.1 % / Av σ(I) over netI: 27.86 / Number: 669906 / R_merge(I) obs: 0.108 / Χ²: 1.26 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 44503 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.75	50	99	1	0.084	2.205	13.9
3.77	4.75	100	1	0.08	1.68	14.1
3.29	3.77	100	1	0.091	1.804	14.4
2.99	3.29	100	1	0.102	1.782	14.6
2.78	2.99	100	1	0.11	1.67	14.9
2.61	2.78	100	1	0.121	1.631	14.9
2.48	2.61	100	1	0.132	1.552	15.1
2.38	2.48	100	1	0.145	1.517	15.2
2.28	2.38	100	1	0.152	1.393	15.3
2.2	2.28	100	1	0.169	1.344	15.3
2.14	2.2	100	1	0.187	1.285	15.4
2.07	2.14	100	1	0.208	1.162	15.5
2.02	2.07	100	1	0.236	1.049	15.5
1.97	2.02	100	1	0.263	0.963	15.6
1.93	1.97	100	1	0.315	0.841	15.6
1.89	1.93	100	1	0.367	0.768	15.6
1.85	1.89	100	1	0.421	0.699	15.6
1.81	1.85	100	1	0.516	0.663	15.5
1.78	1.81	100	1	0.611	0.617	15.3
1.75	1.78	100	1	0.737	0.59	14

Reflection

Resolution: 1.75→50 Å / Num. all: 44503 / Num. obs: 44503 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / B_iso Wilson estimate: 27.4 Å² / R_merge(I) obs: 0.108 / Χ²: 1.257 / Net I/σ(I): 8.1

Reflection shell

Resolution: 1.75→1.78 Å / Redundancy: 14 % / R_merge(I) obs: 0.737 / Num. unique all: 2200 / Χ²: 0.59 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.75 Å / D res low: 50 Å / FOM : 0.319 / FOM acentric: 0.334 / FOM centric: 0.144 / Reflection: 44479 / Reflection acentric: 40944 / Reflection centric: 3535

Phasing MAD set

Highest resolution: 1.75 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.35	1	0.2	0.2	0	0	40944	3535
2	0.99	0.97	17.9	28.8	0.31	0.24	37564	3338

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	11.25-50	1.15	1	0.6	0.5	0	0	119	71
1	6.33-11.25	1.14	1	0.6	0.4	0	0	650	179
1	4.41-6.33	1.12	1	0.5	0.4	0	0	1647	286
1	3.38-4.41	1.01	1	0.4	0.4	0	0	3077	393
1	2.74-3.38	1.22	1	0.2	0.2	0	0	4977	504
1	2.31-2.74	1.48	1	0.1	0.1	0	0	7336	608
1	1.99-2.31	1.88	1	0.1	0	0	0	10134	706
1	1.75-1.99	3.71	1	0.1	0	0	0	13004	788
2	11.25-50	0.97	0.86	30.7	32.4	0.96	0.78	118	68
2	6.33-11.25	0.96	0.89	28	32.1	0.77	0.55	648	178
2	4.41-6.33	0.98	0.95	32.7	46	0.51	0.32	1647	286
2	3.38-4.41	0.99	0.98	38.5	52.7	0.32	0.22	3077	393
2	2.74-3.38	0.99	0.97	26.3	36.5	0.3	0.19	4977	504
2	2.31-2.74	0.99	0.98	17.5	24.6	0.28	0.19	7335	608
2	1.99-2.31	0.99	0.98	12.9	18.6	0.23	0.16	10118	706
2	1.75-1.99	0.99	0.99	9.4	13.2	0.19	0.13	9644	595

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	32.55291	0.33	0.303	0.135	0
2	Se	27.16078	0.069	0.598	0.157	0
3	Se	28.21307	0.781	0.711	0.024	0
4	Se	34.65968	0.446	0.142	0.153	0
5	Se	32.45583	0.565	0.064	0.197	0
6	Se	26.17634	0.047	0.607	0.103	0
7	Se	57.38	0.924	0.621	0.059	0
8	Se	30.31521	0.33	0.304	0.137	-0.099
9	Se	19.24448	0.069	0.598	0.156	-0.092
10	Se	23.22334	0.782	0.712	0.025	-0.065
11	Se	28.62639	0.446	0.142	0.154	-0.093
12	Se	38.59265	0.567	0.064	0.196	-0.138
13	Se	18.35464	0.047	0.607	0.103	-0.062

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
11.25-50	0.512	0.632	0.311	190	119	71
6.33-11.25	0.551	0.617	0.315	829	650	179
4.41-6.33	0.506	0.553	0.237	1933	1647	286
3.38-4.41	0.434	0.468	0.17	3470	3077	393
2.74-3.38	0.445	0.473	0.169	5481	4977	504
2.31-2.74	0.406	0.428	0.143	7944	7336	608
1.99-2.31	0.306	0.319	0.119	10840	10134	706
1.75-1.99	0.159	0.165	0.051	13792	13004	788

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 44479

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.07-100	57.4	0.762	502
6.15-8.07	50.7	0.899	618
5.16-6.15	48.3	0.909	744
4.53-5.16	53.4	0.931	854
4.09-4.53	52.8	0.911	961
3.75-4.09	56.7	0.91	1056
3.49-3.75	56.6	0.904	1116
3.28-3.49	58.2	0.872	1199
3.1-3.28	58.6	0.882	1273
2.94-3.1	57.2	0.897	1342
2.81-2.94	57.8	0.882	1406
2.7-2.81	56.6	0.896	1457
2.59-2.7	56.4	0.9	1512
2.5-2.59	58	0.906	1566
2.42-2.5	57.5	0.909	1624
2.34-2.42	57.5	0.914	1683
2.28-2.34	58.2	0.898	1718
2.21-2.28	58.7	0.9	1793
2.15-2.21	59.7	0.892	1841
2.1-2.15	63	0.88	1851
2.05-2.1	62.2	0.881	1932
2.01-2.05	67	0.881	1940
1.96-2.01	66.3	0.872	2010
1.92-1.96	67.6	0.871	2042
1.88-1.92	67.8	0.868	2061
1.85-1.88	70.1	0.863	2159
1.81-1.85	74.5	0.858	2158
1.78-1.81	77.5	0.835	2217
1.75-1.78	81.2	0.745	1844

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.8→38.42 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.962 / WR_factor R_free: 0.186 / WR_factor R_work: 0.161 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.926 / SU B: 3.643 / SU ML: 0.053 / SU R Cruickshank DPI: 0.094 / SU R_free: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.176	2071	5 %	RANDOM
R_work	0.153	-	-	-
all	0.154	41262	-	-
obs	0.154	41262	99.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 66.46 Å² / B_iso mean: 21.262 Å² / B_iso min: 11.53 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.16 Å²	0 Å²	0 Å²
2-	-	0.43 Å²	0 Å²
3-	-	-	0.73 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→38.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2572	0	39	362	2973

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2731
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1862
X-RAY DIFFRACTION	r_angle_refined_deg	1.355	1.971	3697
X-RAY DIFFRACTION	r_angle_other_deg	0.924	3	4571
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.958	5	352
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.108	25.504	129
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.511	15	488
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.107	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	410
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3046
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	526
X-RAY DIFFRACTION	r_mcbond_it	0.772	1.5	1671
X-RAY DIFFRACTION	r_mcbond_other	0.229	1.5	678
X-RAY DIFFRACTION	r_mcangle_it	1.428	2	2695
X-RAY DIFFRACTION	r_scbond_it	2.405	3	1060
X-RAY DIFFRACTION	r_scangle_it	3.92	4.5	990

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.22	148	-
R_work	0.215	2847	-
all	-	2995	-
obs	-	-	100 %

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	0.7336	-0.3961	0.0544	0.7381	0.4193	1.2877	-0.0542	-0.0384	0.0392	0.1076	0.0322	0.0311	-0.0178	-0.1076	0.022	0.0422	0.0272	0.0186	0.063	-0.0015	0.0444	31.3858	11.2079	21.1971
2	0.5251	-0.3135	-0.0055	0.9721	0.0984	0.8014	-0.0476	0.0349	0.1571	-0.0682	0.0196	-0.0582	-0.1282	-0.0571	0.028	0.0509	0.023	-0.0186	0.0574	0.0088	0.0721	33.7406	19.7305	4.2486
3	0.9341	-0.8364	0.4369	1.1193	0.4641	2.2375	-0.0472	-0.153	0.1345	0.0481	0.1568	-0.0918	-0.26	-0.1361	-0.1096	0.0817	0.056	0.0302	0.0613	-0.0051	0.1029	30.6119	21.647	24.4764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 88
2	X-RAY DIFFRACTION	2	A	89 - 274
3	X-RAY DIFFRACTION	3	A	275 - 329

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