PDB-2fiq: Crystal structure of putative tagatose 6-phosphate kinase

ID or keywords:

Entry

Database: PDB / ID: 2fiq

Title

Crystal structure of putative tagatose 6-phosphate kinase

Components

putative tagatose 6-phosphate kinase 1

Keywords

TRANSFERASE / structural genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC

Function / homology

Function and homology information

galactitol catabolic process / D-tagatose 6-phosphate catabolic process / catalytic activity
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.25 Å

Authors

Ramagopal, U.A. / Fedorov, E. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)

Citation

Journal: To be Published
Title: Crystal structure of putative tagatose 6-phosphate kinase
Authors: Ramagopal, U.A. / Fedorov, E. / Almo, S.C.

History

Deposition	Dec 30, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 4, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Feb 3, 2021	Group: Database references / Derived calculations / Structure summary Category: audit_author / struct_conn / struct_ref_seq_dif Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2fiq.cif.gz	335.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2fiq.ent.gz	286.3 KB	Display	PDB format
PDBx/mmJSON format	2fiq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2fiq_validation.pdf.gz	444.5 KB	Display	wwPDB validaton report
Full document	2fiq_full_validation.pdf.gz	465.9 KB	Display
Data in XML	2fiq_validation.xml.gz	63.6 KB	Display
Data in CIF	2fiq_validation.cif.gz	91 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fi/2fiq ftp://data.pdbj.org/pub/pdb/validation_reports/fi/2fiq	HTTPS FTP

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Related structure data

Similar structure data	3txv-2 1noy-d 6h6x-d 4pxb-d 4ruh-d 4wgg-d 4xdn-d 1xx9-d 3aic-6 5w94-1 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	TargetDB: NYSGXRC-T2029

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: putative tagatose 6-phosphate kinase 1

B: putative tagatose 6-phosphate kinase 1

C: putative tagatose 6-phosphate kinase 1

D: putative tagatose 6-phosphate kinase 1

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

1

A: putative tagatose 6-phosphate kinase 1

B: putative tagatose 6-phosphate kinase 1

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

2

C: putative tagatose 6-phosphate kinase 1

D: putative tagatose 6-phosphate kinase 1

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	92.352, 100.001, 206.549
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ILE	HIS	4	A	A	5 - 88	5 - 88
2	1	ILE	HIS	4	B	B	5 - 88	5 - 88
3	1	ILE	HIS	4	C	C	5 - 88	5 - 88
4	1	ILE	HIS	4	D	D	5 - 88	5 - 88
1	2	LEU	GLU	6	A	A	89 - 139	89 - 139
2	2	LEU	GLU	6	B	B	89 - 139	89 - 139
3	2	LEU	GLU	6	C	C	89 - 139	89 - 139
4	2	LEU	GLU	6	D	D	89 - 139	89 - 139
1	3	THR	VAL	4	A	A	140 - 172	140 - 172
2	3	THR	VAL	4	B	B	140 - 172	140 - 172
3	3	THR	VAL	4	C	C	140 - 172	140 - 172
4	3	THR	VAL	4	D	D	140 - 172	140 - 172
1	4	VAL	ALA	4	A	A	185 - 283	185 - 283
2	4	HIS	ALA	4	B	B	186 - 283	186 - 283
3	4	VAL	ALA	4	C	C	185 - 283	185 - 283
4	4	VAL	ALA	4	C	C	185 - 283	185 - 283
1	5	LEU	CYS	4	A	A	284 - 418	284 - 418
2	5	LEU	CYS	4	B	B	284 - 418	284 - 418
3	5	LEU	CYS	4	C	C	284 - 418	284 - 418
4	5	LEU	CYS	4	D	D	284 - 418	284 - 418

NCS ensembles :

ID
1
2
3
4
5

Details

The biological unit apperas to be a dimer. There are two assumed biological uints in the asymmetric unit (chains A & B and chains C & D)

#1: Protein	putative tagatose 6-phosphate kinase 1 Mass: 47543.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs2898 / Production host: Escherichia coli (E. coli) References: UniProt: P37191, UniProt: Q8X7H4*PLUS, EC: 2.7.1.101
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 724 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 50.93 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PED 3350, 10 mM NaCl, 50mM MgCl2, Tris-Bis pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	NSLS	X29A	1	1.074
SYNCHROTRON	NSLS	X9A	2	0.98

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2005

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.074	1
2	0.98	1

Reflection

Redundancy: 3.6 % / Number: 160766 / R_merge(I) obs: 0.084 / Χ²: 1.051 / D res high: 2.32 Å / D res low: 50 Å / % possible obs: 99.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5	50	99.8	1	0.046	1.296	3.6
3.97	5	99.9	1	0.052	1.321	3.6
3.47	3.97	99.9	1	0.058	1.186	3.6
3.15	3.47	99.9	1	0.095	1.189	3.7
2.92	3.15	100	1	0.151	1.059	3.7
2.75	2.92	100	1	0.232	0.978	3.7
2.61	2.75	100	1	0.362	0.958	3.6
2.5	2.61	100	1	0.49	0.849	3.7
2.4	2.5	100	1	0.609	0.837	3.6
2.32	2.4	94.5	1	0.75	0.825	3.4

Reflection

Resolution: 2.25→50 Å / Num. all: 89439 / Num. obs: 89439 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / B_iso Wilson estimate: 38.075 Å² / R_merge(I) obs: 0.059 / R_sym value: 0.046 / Χ²: 0.717 / Net I/σ(I): 20.8

Reflection shell

Resolution: 2.25→2.33 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.335 / Mean I/σ(I) obs: 3.54 / Num. unique all: 8902 / R_sym value: 0.277 / Χ²: 0.518 / % possible all: 99

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.2.0005	refinement
PDB_EXTRACT	1.701	data extraction
CBASS		data collection
SHELXE		model building
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.25→50 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.928 / SU B: 12.213 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.294 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.233	4483	5 %	RANDOM
R_work	0.187	-	-	-
all	0.189	89327	-	-
obs	0.187	89327	97.72 %	-

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: 37.744 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.06 Å²	0 Å²	0 Å²
2-	-	-1.07 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12957	0	0	724	13681

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	13359
X-RAY DIFFRACTION	r_angle_refined_deg	1.38	1.943	18153
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.816	5	1656
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.905	23.584	639
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.545	15	2235
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.423	15	103
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	2029
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10239
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	6304
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	9250
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	881
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.228	0.2	69
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.172	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	0.758	1.5	8496
X-RAY DIFFRACTION	r_mcangle_it	1.017	2	13320
X-RAY DIFFRACTION	r_scbond_it	1.93	3	5536
X-RAY DIFFRACTION	r_scangle_it	2.663	4.5	4833

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	624	MEDIUM POSITIONAL	0.32	0.5
1	2	B	624	MEDIUM POSITIONAL	0.33	0.5
1	3	C	624	MEDIUM POSITIONAL	0.46	0.5
1	4	D	624	MEDIUM POSITIONAL	0.28	0.5
1	1	A	624	MEDIUM THERMAL	0.64	2
1	2	B	624	MEDIUM THERMAL	0.53	2
1	3	C	624	MEDIUM THERMAL	0.58	2
1	4	D	624	MEDIUM THERMAL	0.55	2
2	1	A	382	LOOSE POSITIONAL	0.41	5
2	2	B	382	LOOSE POSITIONAL	0.43	5
2	3	C	382	LOOSE POSITIONAL	0.44	5
2	4	D	382	LOOSE POSITIONAL	0.44	5
2	1	A	382	LOOSE THERMAL	1.41	10
2	2	B	382	LOOSE THERMAL	1.69	10
2	3	C	382	LOOSE THERMAL	1.04	10
2	4	D	382	LOOSE THERMAL	2.04	10
3	1	A	235	MEDIUM POSITIONAL	0.36	0.5
3	2	B	235	MEDIUM POSITIONAL	0.43	0.5
3	3	C	235	MEDIUM POSITIONAL	0.68	0.5
3	4	D	235	MEDIUM POSITIONAL	0.42	0.5
3	1	A	235	MEDIUM THERMAL	0.58	2
3	2	B	235	MEDIUM THERMAL	0.5	2
3	3	C	235	MEDIUM THERMAL	0.68	2
3	4	D	235	MEDIUM THERMAL	0.55	2
4	1	A	745	MEDIUM POSITIONAL	0.55	0.5
4	2	B	745	MEDIUM POSITIONAL	0.47	0.5
4	3	C	745	MEDIUM POSITIONAL	0.35	0.5
4	4	D	745	MEDIUM POSITIONAL	0.35	0.5
4	1	A	745	MEDIUM THERMAL	0.85	2
4	2	B	745	MEDIUM THERMAL	0.65	2
4	3	C	745	MEDIUM THERMAL	0.35	2
4	4	D	745	MEDIUM THERMAL	0.35	2
5	1	A	1088	MEDIUM POSITIONAL	0.32	0.5
5	2	B	1088	MEDIUM POSITIONAL	0.39	0.5
5	3	C	1088	MEDIUM POSITIONAL	0.43	0.5
5	4	D	1088	MEDIUM POSITIONAL	0.38	0.5
5	1	A	1088	MEDIUM THERMAL	0.75	2
5	2	B	1088	MEDIUM THERMAL	0.76	2
5	3	C	1088	MEDIUM THERMAL	0.86	2
5	4	D	1088	MEDIUM THERMAL	0.93	2

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	312	-
R_work	0.213	6284	-
obs	-	6596	98.54 %

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	0.989	0.5324	-1.2043	1.8347	-1.227	3.22	0.1308	-0.1993	0.1098	0.2287	-0.1768	-0.2016	-0.308	0.2013	0.0459	-0.2624	-0.062	0.048	0.0399	0.0055	-0.1309	84.015	87.988	59.065
2	1.1419	0.4447	-0.4707	1.2743	-0.2615	0.9402	0.0368	0.0606	0.1104	0.1488	0.0119	0.1113	-0.0652	-0.0256	-0.0487	-0.2922	0.0062	0.0484	0.0053	0.011	-0.2118	96.428	96.267	34.952
3	1.61	0.1493	0.3264	2.8582	2.5357	3.0226	-0.1193	0.2638	-0.0297	-0.424	0.0552	0.0358	-0.208	0.1097	0.0641	-0.1613	-0.0714	-0.0503	0.1953	-0.0503	-0.0173	94.385	67.947	1.129
4	1.9005	0.7765	0.0476	1.842	0.343	0.9463	0.0059	0.3166	-0.361	-0.0541	0.0971	-0.1229	0.0977	0.075	-0.103	-0.3004	0.0121	-0.0035	0.1048	-0.0672	-0.1785	106.426	84.503	20.638
5	2.6042	0.5735	2.119	1.5425	1.1424	2.8343	0.1289	-0.2103	-0.0164	0.3639	-0.161	-0.0568	0.1575	-0.0527	0.0321	-0.2413	-0.0896	-0.0128	0.1243	-0.0367	-0.1295	147.75	120.363	49.266
6	1.3846	0.3115	0.3248	1.614	-0.0557	1.0286	0.0322	0.0815	-0.1415	0.0603	0.0425	-0.1124	0.0734	0.1381	-0.0747	-0.3505	0.0151	-0.0097	0.052	-0.0221	-0.2447	130.485	109.22	29.766
7	3.0463	0.2633	-1.5713	1.2869	-0.5244	3.5996	0.0413	0.7523	0.0917	-0.146	0.0787	0.161	-0.1255	-0.7293	-0.12	-0.3384	0.0082	0.0003	0.3863	0.1136	-0.2052	121.416	133.981	-6.23
8	1.0168	0.4479	-0.1082	0.7518	-0.293	1.3215	-0.0003	0.2251	0.0597	-0.0015	0.0815	0.0684	0.0175	-0.0611	-0.0812	-0.3562	0.0105	-0.0028	0.0693	0.0249	-0.2757	116.803	119.625	17.425

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	1 - 283	1 - 283
2	2	A	A	284 - 419	284 - 419
3	3	B	B	1 - 283	1 - 283
4	4	B	B	284 - 419	284 - 419
5	5	C	C	1 - 283	1 - 283
6	6	C	C	284 - 419	284 - 419
7	7	D	D	1 - 283	1 - 283
8	8	D	D	284 - 419	284 - 419

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