PDB-2f8j: Crystal structure of Histidinol-phosphate aminotransferase (EC 2....

ID or keywords:

Entry

Database: PDB / ID: 2f8j

Title

Crystal structure of Histidinol-phosphate aminotransferase (EC 2.6.1.9) (Imidazole acetol-phosphate transferase) (tm1040) from Thermotoga maritima at 2.40 A resolution

Components

Histidinol-phosphate aminotransferase

Keywords

TRANSFERASE / tm1040 / Histidinol-phosphate aminotransferase (EC 2.6.1.9) (Imidazole acetol-phosphate transferase / Structural Genomics / PSI / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG

Function / homology

Function and homology information

histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.4 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of Histidinol-phosphate aminotransferase (EC 2.6.1.9) (Imidazole acetol-phosphate transferase) (tm1040) from Thermotoga maritima at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Dec 2, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 21, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Jan 25, 2023	Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Sep 20, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Remark 300

BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2f8j.cif.gz	282.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2f8j.ent.gz	224.3 KB	Display	PDB format
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Validation report

Summary document	2f8j_validation.pdf.gz	497.7 KB	Display	wwPDB validaton report
Full document	2f8j_full_validation.pdf.gz	516 KB	Display
Data in XML	2f8j_validation.xml.gz	51.2 KB	Display
Data in CIF	2f8j_validation.cif.gz	71.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f8/2f8j ftp://data.pdbj.org/pub/pdb/validation_reports/f8/2f8j	HTTPS FTP

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Related structure data

Related structure data	1uu0S S: Starting model for refinement
Similar structure data	3ei7-d 4aoa-d 2o53-d 4r5z-2 1uu0-1 3ei6-d 1uu1-1 2p82-1 2z1y-d 1uu0-2 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: 359801

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Histidinol-phosphate aminotransferase

B: Histidinol-phosphate aminotransferase

C: Histidinol-phosphate aminotransferase

D: Histidinol-phosphate aminotransferase

hetero molecules

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

1

A: Histidinol-phosphate aminotransferase

B: Histidinol-phosphate aminotransferase

hetero molecules

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

2

C: Histidinol-phosphate aminotransferase

D: Histidinol-phosphate aminotransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	145.156, 187.453, 54.316
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-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	MET	MET	LYS	LYS	5	A	A	1 - 21	13 - 33
2	1	ASN	ASN	LYS	LYS	5	B	B	2 - 21	14 - 33
3	1	MET	MET	LYS	LYS	5	C	C	1 - 21	13 - 33
4	1	ASN	ASN	LYS	LYS	5	D	D	2 - 21	14 - 33
5	2	THR	THR	VAL	VAL	2	A	A	22 - 38	34 - 50
6	2	THR	THR	VAL	VAL	2	B	B	22 - 38	34 - 50
7	2	THR	THR	VAL	VAL	2	C	C	22 - 38	34 - 50
8	2	THR	THR	VAL	VAL	2	D	D	22 - 38	34 - 50
9	3	ASP	ASP	LEU	LEU	6	A	A	39 - 45	51 - 57
10	3	ASP	ASP	LEU	LEU	6	B	B	39 - 45	51 - 57
11	3	ASP	ASP	LEU	LEU	6	C	C	39 - 45	51 - 57
12	3	ASP	ASP	LEU	LEU	6	D	D	39 - 45	51 - 57
13	4	ASN	ASN	LEU	LEU	4	A	A	46 - 69	58 - 81
14	4	ASN	ASN	LEU	LEU	4	B	B	46 - 69	58 - 81
15	4	ASN	ASN	LEU	LEU	4	C	C	46 - 69	58 - 81
16	4	ASN	ASN	LEU	LEU	4	D	D	46 - 69	58 - 81
17	5	ASP	ASP	PHE	PHE	3	A	A	70 - 73	82 - 85
18	5	ASP	ASP	PHE	PHE	3	B	B	70 - 73	82 - 85
19	5	ASP	ASP	PHE	PHE	3	C	C	70 - 73	82 - 85
20	5	ASP	ASP	PHE	PHE	3	D	D	70 - 73	82 - 85
21	6	LEU	LEU	ILE	ILE	2	A	A	74 - 111	86 - 123
22	6	LEU	LEU	ILE	ILE	2	B	B	74 - 111	86 - 123
23	6	LEU	LEU	ILE	ILE	2	C	C	74 - 111	86 - 123
24	6	LEU	LEU	ILE	ILE	2	D	D	74 - 111	86 - 123
25	7	PHE	PHE	GLU	GLU	3	A	A	112 - 138	124 - 150
26	7	PHE	PHE	GLU	GLU	3	B	B	112 - 138	124 - 150
27	7	PHE	PHE	GLU	GLU	3	C	C	112 - 138	124 - 150
28	7	PHE	PHE	GLU	GLU	3	D	D	112 - 138	124 - 150
29	8	GLU	GLU	PHE	PHE	2	A	A	138 - 155	150 - 167
30	8	GLU	GLU	PHE	PHE	2	B	B	138 - 155	150 - 167
31	8	GLU	GLU	PHE	PHE	2	C	C	138 - 155	150 - 167
32	8	GLU	GLU	PHE	PHE	2	D	D	138 - 155	150 - 167
33	9	GLU	GLU	GLY	GLY	4	A	A	156 - 167	168 - 179
34	9	GLU	GLU	GLY	GLY	4	B	B	156 - 167	168 - 179
35	9	GLU	GLU	GLY	GLY	4	C	C	156 - 167	168 - 179
36	9	GLU	GLU	GLY	GLY	4	D	D	156 - 167	168 - 179
37	10	ALA	ALA	SER	SER	1	A	A	168 - 183	180 - 195
38	10	ALA	ALA	SER	SER	1	B	B	168 - 183	180 - 195
39	10	ALA	ALA	SER	SER	1	C	C	168 - 183	180 - 195
40	10	ALA	ALA	SER	SER	1	D	D	168 - 183	180 - 195
41	11	TYR	TYR	ASN	ASN	4	A	A	184 - 193	196 - 205
42	11	TYR	TYR	ASN	ASN	4	B	B	184 - 193	196 - 205
43	11	TYR	TYR	ASN	ASN	4	C	C	184 - 193	196 - 205
44	11	TYR	TYR	ASN	ASN	4	D	D	184 - 193	196 - 205
45	12	LEU	LEU	GLN	GLN	1	A	A	194 - 238	206 - 250
46	12	LEU	LEU	GLN	GLN	1	B	B	194 - 238	206 - 250
47	12	LEU	LEU	GLN	GLN	1	C	C	194 - 238	206 - 250
48	12	LEU	LEU	GLN	GLN	1	D	D	194 - 238	206 - 250
49	13	MET	MET	LYS	LYS	2	A	A	239 - 266	251 - 278
50	13	MET	MET	LYS	LYS	2	B	B	239 - 266	251 - 278
51	13	MET	MET	LYS	LYS	2	C	C	239 - 266	251 - 278
52	13	MET	MET	LYS	LYS	2	D	D	239 - 266	251 - 278
53	14	SER	SER	VAL	VAL	1	A	A	267 - 286	279 - 298
54	14	SER	SER	VAL	VAL	1	B	B	267 - 286	279 - 298
55	14	SER	SER	VAL	VAL	1	C	C	267 - 286	279 - 298
56	14	SER	SER	VAL	VAL	1	D	D	267 - 286	279 - 298
57	15	PHE	PHE	PHE	PHE	5	A	A	287 - 334	299 - 346
58	15	PHE	PHE	PHE	PHE	5	B	B	287 - 334	299 - 346
59	15	PHE	PHE	PHE	PHE	5	C	C	287 - 334	299 - 346
60	15	PHE	PHE	PHE	PHE	5	D	D	287 - 334	299 - 346

#1: Protein	Histidinol-phosphate aminotransferase / Imidazole acetol-phosphate transaminase Mass: 40812.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisC / Production host: Escherichia coli (E. coli) References: UniProt: Q9X0D0, histidinol-phosphate transaminase
#2: Chemical	ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₃N₂O₅P
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.4 Å³/Da / Density % sol: 48.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5 Details: 0.2M MgCl2, 20.0% PEG-1000, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 1.000001 / Wavelength: 1.000001 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2005 / Details: double crystal monochromator

Radiation

Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.000001 Å / Relative weight: 1

Reflection

Resolution: 2.4→29.8 Å / Num. obs: 54470 / % possible obs: 91.7 % / Redundancy: 2.7 % / R_merge(I) obs: 0.079 / Χ²: 0.988 / Net I/σ(I): 9.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Χ²	% possible all
2.4-2.44	2.6	0.562	1.8	2653	1.049	90.1
2.44-2.49	2.7	0.542		2707	1.028	92.6
2.49-2.53	2.7	0.455		2692	1.044	93.3
2.53-2.59	2.6	0.416		2806	0.972	94
2.59-2.64	2.7	0.368		2691	0.964	92.7
2.64-2.7	2.6	0.324		2706	0.992	93.1
2.7-2.77	2.7	0.268		2715	1.046	92.3
2.77-2.85	2.7	0.224		2757	1.042	93.8
2.85-2.93	2.7	0.186		2735	0.945	93.1
2.93-3.02	2.7	0.156		2737	0.914	92.6
3.02-3.13	2.7	0.13		2715	1.056	93.3
3.13-3.26	2.7	0.107		2751	1.036	92.8
3.26-3.41	2.7	0.081		2712	0.923	91.1
3.41-3.58	2.7	0.073		2719	0.94	92.3
3.58-3.81	2.7	0.064		2708	0.976	91.1
3.81-4.1	2.7	0.057		2698	0.912	90.8
4.1-4.52	2.6	0.058		2699	0.988	89.3
4.52-5.17	2.6	0.059		2738	0.847	90.5
5.17-6.51	2.7	0.055		2715	1.06	88.8
6.51-50	2.6	0.055		2816	1.022	86.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
SCALA		data scaling
PDB_EXTRACT	1.601	data extraction
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1uu0

1uu0

Resolution: 2.4→29.6 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.939 / SU B: 15.797 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.549 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.THE BOUND COFACTOR ON ALL FOUR SUBUNITS WERE MODELED AS PYRIDOXAMINE PHOSPHATE. HOWEVER, THE ELECTRON DENSITIES AT THE ACTIVE SITE ARE ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	2745	5 %	RANDOM
R_work	0.182	-	-	-
all	0.185	-	-	-
obs	0.18469	51626	91.54 %	-

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: 53.956 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.09 Å²	0 Å²	0 Å²
2-	-	-1.39 Å²	0 Å²
3-	-	-	-0.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→29.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10520	0	116	339	10975

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	10893
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9953
X-RAY DIFFRACTION	r_angle_refined_deg	1.228	1.968	14729
X-RAY DIFFRACTION	r_angle_other_deg	0.798	3	22845
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.902	5	1340
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.403	22.888	509
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.307	15	1756
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.709	15	88
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1608
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	12199
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2453
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	2117
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	9840
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	5417
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	6364
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	399
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.056	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.14	0.2	26
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.257	0.2	78
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.154	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	1.178	3	6843
X-RAY DIFFRACTION	r_mcbond_other	0.302	3	2682
X-RAY DIFFRACTION	r_mcangle_it	1.896	5	10756
X-RAY DIFFRACTION	r_scbond_it	3.733	8	4563
X-RAY DIFFRACTION	r_scangle_it	5.549	11	3971

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1933	TIGHT POSITIONAL	0.03	0.05
2	B	1933	TIGHT POSITIONAL	0.04	0.05
3	C	1933	TIGHT POSITIONAL	0.04	0.05
4	D	1933	TIGHT POSITIONAL	0.02	0.05
1	A	1943	MEDIUM POSITIONAL	0.36	0.5
2	B	1943	MEDIUM POSITIONAL	0.36	0.5
3	C	1943	MEDIUM POSITIONAL	0.47	0.5
4	D	1943	MEDIUM POSITIONAL	0.35	0.5
1	A	794	LOOSE POSITIONAL	0.7	5
2	B	794	LOOSE POSITIONAL	0.7	5
3	C	794	LOOSE POSITIONAL	0.83	5
4	D	794	LOOSE POSITIONAL	0.72	5
1	A	1933	TIGHT THERMAL	0.09	0.5
2	B	1933	TIGHT THERMAL	0.1	0.5
3	C	1933	TIGHT THERMAL	0.09	0.5
4	D	1933	TIGHT THERMAL	0.07	0.5
1	A	1943	MEDIUM THERMAL	0.72	2
2	B	1943	MEDIUM THERMAL	0.74	2
3	C	1943	MEDIUM THERMAL	0.71	2
4	D	1943	MEDIUM THERMAL	0.53	2
1	A	794	LOOSE THERMAL	2.54	10
2	B	794	LOOSE THERMAL	2.15	10
3	C	794	LOOSE THERMAL	2.59	10
4	D	794	LOOSE THERMAL	2.04	10

LS refinement shell

Resolution: 2.395→2.457 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.262	211	-
R_work	0.224	3707	-
obs	-	-	90.09 %

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	0.9225	-0.1859	0.274	1.1497	-0.2265	0.9647	0.0101	-0.0133	0.0549	0.0774	-0.0166	-0.2942	-0.0977	0.1143	0.0064	-0.1501	-0.0329	-0.0206	-0.1486	0.0034	-0.1312	-27.8929	14.2309	6.3596
2	1.2964	-0.3751	0.2626	0.9684	-0.0495	1.7224	0.1005	0.0358	0.0241	-0.115	0.0029	0.0444	-0.1095	-0.1158	-0.1034	-0.1498	0.0005	0.0075	-0.1485	0.0288	-0.2129	-54.4683	9.915	-12.0258
3	1.5097	0.244	0.6399	1.7575	0.0192	0.9688	-0.009	0.1141	-0.0995	-0.0477	0.0006	0.0724	0.0463	0.041	0.0084	-0.1387	-0.0205	0.0252	-0.1619	-0.0147	-0.1689	-23.8672	59.3627	-12.2363
4	2.0996	-0.8213	0.084	2.4583	0.1046	0.9322	-0.0852	-0.1843	-0.3164	0.3464	-0.024	1.0905	0.081	-0.3414	0.1092	-0.0352	-0.031	0.1753	0.0152	-0.0275	0.4009	-55.4474	62.3648	-6.4216

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	0 - 334	12 - 346
2	2	B	B	2 - 334	14 - 346
3	3	C	C	1 - 334	13 - 346
4	4	D	D	4 - 334	16 - 346

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi