PDB-2jg5: CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOFRUCTOKINASE FROM STAPHYLO...

ID or keywords:

Entry

Database: PDB / ID: 2jg5

Title

CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOFRUCTOKINASE FROM STAPHYLOCOCCUS AUREUS

Components

FRUCTOSE 1-PHOSPHATE KINASE

Keywords

TRANSFERASE / KINASE / 1-PHOSPHOFRUCTOKINASE

Function / homology

Function and homology information

1-phosphofructokinase activity / lactose metabolic process / tagatose-6-phosphate kinase / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / small molecule metabolic process / carbohydrate catabolic process / ATP binding / cytosol
Similarity search - Function

Biological species

STAPHYLOCOCCUS AUREUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Yan, X. / Carter, L.G. / Johnson, K.A. / Liu, H. / Dorward, M. / McMahon, S.A. / Oke, M. / Powers, H. / Coote, P.J. / Naismith, J.H.

Citation

Journal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...

History

Deposition	Feb 8, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 27, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Sep 28, 2011	Group: Database references / Derived calculations / Structure summary
Revision 1.3	Mar 11, 2020	Group: Derived calculations / Other Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop Item: _pdbx_database_status.status_code_sf
Revision 1.4	Dec 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2jg5.cif.gz	125.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2jg5_validation.pdf.gz	439.5 KB	Display	wwPDB validaton report
Full document	2jg5_full_validation.pdf.gz	447.4 KB	Display
Data in XML	2jg5_validation.xml.gz	23.4 KB	Display
Data in CIF	2jg5_validation.cif.gz	33 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jg/2jg5 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jg5	HTTPS FTP

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Related structure data

Related structure data	2ivyC 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C 2abqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6g9p-d 3eqr-1 3zwk-d 4hzr-d 3zw7-d 6y6u-d 1c1x-1 1oph-d 3nps-d 6g9s-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: FRUCTOSE 1-PHOSPHATE KINASE

B: FRUCTOSE 1-PHOSPHATE KINASE

65.1 kDa, 2 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)	85.010, 160.260, 40.740
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:

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	ASN	ASN	4	A	A	1 - 8	1 - 8
2	1	1	MET	MET	ASN	ASN	4	B	B	1 - 8	1 - 8
1	1	2	LYS	LYS	GLY	GLY	4	A	A	38 - 61	38 - 61
2	1	2	LYS	LYS	GLY	GLY	4	B	B	38 - 61	38 - 61
1	2	2	PRO	PRO	VAL	VAL	4	A	A	106 - 159	106 - 159
2	2	2	PRO	PRO	VAL	VAL	4	B	B	106 - 159	106 - 159
1	3	2	ALA	ALA	LEU	LEU	4	A	A	167 - 176	167 - 176
2	3	2	ALA	ALA	LEU	LEU	4	B	B	167 - 176	167 - 176
1	4	2	TYR	TYR	THR	THR	4	A	A	202 - 279	202 - 279
2	4	2	TYR	TYR	THR	THR	4	B	B	202 - 279	202 - 279
1	5	2	THR	THR	GLN	GLN	4	A	A	287 - 297	287 - 297
2	5	2	THR	THR	GLN	GLN	4	B	B	287 - 297	287 - 297
1	6	2	PRO	PRO	ILE	ILE	4	A	A	63 - 68	63 - 68
2	6	2	PRO	PRO	ILE	ILE	4	B	B	63 - 68	63 - 68
1	7	2	THR	THR	ILE	ILE	4	A	A	70 - 81	70 - 81
2	7	2	THR	THR	ILE	ILE	4	B	B	70 - 81	70 - 81
1	1	3	PHE	PHE	PHE	PHE	4	A	A	177 - 189	177 - 189
2	1	3	PHE	PHE	PHE	PHE	4	B	B	177 - 189	177 - 189
1	1	4	VAL	VAL	GLY	GLY	4	A	A	298 - 305	298 - 305
2	1	4	VAL	VAL	GLY	GLY	4	B	B	298 - 305	298 - 305
1	1	5	ILE	ILE	LEU	LEU	5	A	A	89 - 93	89 - 93
2	1	5	ILE	ILE	LEU	LEU	5	B	B	89 - 93	89 - 93
1	2	5	GLU	GLU	GLY	GLY	5	A	A	98 - 105	98 - 105
2	2	5	GLU	GLU	GLY	GLY	5	B	B	98 - 105	98 - 105
1	1	6	ASP	ASP	PHE	PHE	5	A	A	12 - 16	12 - 16
2	1	6	ASP	ASP	PHE	PHE	5	B	B	12 - 16	12 - 16
1	2	6	ASN	ASN	TYR	TYR	5	A	A	26 - 32	26 - 32
2	2	6	ASN	ASN	TYR	TYR	5	B	B	26 - 32	26 - 32

NCS ensembles :

ID
1
2
3
4
5
6

NCS oper: (Code: given
Matrix: (-0.99808, -0.00574, -0.06161), (0.00015, -0.99591, 0.09033), (-0.06188, 0.09015, 0.994)
Vector: 1.09623, 158.3727, -8.1911)

#1: Protein	FRUCTOSE 1-PHOSPHATE KINASE Mass: 32555.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MRSA252 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KWK1, EC: 2.7.1.56
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.04 Å³/Da / Density % sol: 40 %
Crystal grow	pH: 5.6 Details: 0.2 M AMMONIUM ACETATE, 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30% W/V PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976
Detector	Type: MARRESEARCH / Detector: CCD / Date: Mar 5, 2006 / Details: MIRRORS
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.28→30 Å / Num. obs: 25486 / % possible obs: 98.1 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / R_merge(I) obs: 0.11 / Net I/σ(I): 11.65
Reflection shell	Resolution: 2.28→2.42 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.11 / Mean I/σ(I) obs: 11.65 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ABQ

2abq

Resolution: 2.3→19.75 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.87 / SU B: 20.902 / SU ML: 0.247 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.276	1290	5.1 %	RANDOM
R_work	0.212	-	-	-
obs	0.215	24100	99.5 %	-

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: 32.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	0 Å²	0 Å²
2-	-	-0.05 Å²	0 Å²
3-	-	-	0.13 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→19.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4572	0	0	130	4702

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4634
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.195	1.964	6294
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.862	5	610
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.892	26.559	186
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.99	15	792
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.671	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	766
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3424
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	2222
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.3	0.2	3296
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	230
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	0.227	0.2	89
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.163	0.2	11
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	0.381	1.5	3094
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.644	2	4910
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.994	3	1679
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.58	4.5	1384
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

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	68	medium positional	0.13	0.5
2	1418	medium positional	0.31	0.5
3	112	medium positional	0.21	0.5
4	55	medium positional	0.35	0.5
5	52	medium positional	0.14	0.5
6	48	medium positional	0.15	0.5
5	45	loose positional	0.58	5
6	53	loose positional	0.83	5
1	68	medium thermal	0.37	2
2	1418	medium thermal	0.47	2
3	112	medium thermal	0.48	2
4	55	medium thermal	0.3	2
5	52	medium thermal	0.26	2
6	48	medium thermal	0.4	2
5	45	loose thermal	0.69	10
6	53	loose thermal	1.29	10

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	75	-
R_work	0.279	1649	-
obs	-	-	94.57 %

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	3.2835	0.1767	-0.5793	4.5263	0.4917	1.0392	-0.0217	-0.0435	0.005	0.3272	0.0496	0.6096	-0.0214	-0.16	-0.0279	-0.0944	-0.0097	-0.045	-0.1062	0.0325	-0.1186	8.8485	68.1168	12.1645
2	1.1677	-0.3673	-0.8821	3.9284	1.5025	1.0973	-0.0355	0.1676	0.0206	-0.2291	0.0836	-0.111	0.0273	0.0443	-0.0481	-0.0745	-0.0147	-0.0697	-0.0617	0.0194	-0.0983	20.4049	55.9232	3.2341
3	1.8704	-1.1833	0.015	7.5555	-0.097	1.0313	-0.2582	-0.0448	0.0519	0.3385	0.2257	-0.4572	0.0019	0.3374	0.0325	-0.1138	-0.0291	0.0174	-0.0283	-0.0432	-0.1015	-8.6693	91.6636	8.9124
4	0.7557	-0.6429	0.7092	2.5771	-1.1987	1.2507	-0.02	0.2057	0.0891	-0.2258	-0.0396	-0.124	0.0125	0.1094	0.0596	-0.0492	-0.0283	0.0639	-0.0068	-0.0308	-0.1042	-20.1567	103.5395	-1.2351
5	6.3323	0.3368	-0.2036	3.2722	-1.121	3.8352	-0.2467	0.9322	-0.5371	-0.4627	0.1123	0.0749	0.2531	-0.1699	0.1344	-0.0178	-0.0766	0.0102	0.0184	-0.1094	-0.0713	-0.4799	73.4024	-6.9891
6	8.0906	0.9373	-2.7995	2.0554	0.8365	2.8883	0.0148	1.0021	0.1679	-0.3531	0.0524	-0.0531	-0.1251	-0.1571	-0.0672	-0.0213	-0.0293	0.0214	-0.0056	0.0219	-0.1313	3.2026	82.2362	-7.6529

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 9
2	X-RAY DIFFRACTION	1	A	38 - 88
3	X-RAY DIFFRACTION	2	A	106 - 306
4	X-RAY DIFFRACTION	3	B	1 - 9
5	X-RAY DIFFRACTION	3	B	38 - 88
6	X-RAY DIFFRACTION	4	B	106 - 306
7	X-RAY DIFFRACTION	5	A	10 - 37
8	X-RAY DIFFRACTION	5	A	89 - 105
9	X-RAY DIFFRACTION	6	B	10 - 37
10	X-RAY DIFFRACTION	6	B	89 - 105

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