PDB-7kqa: Crystal Structure of Glucosamine-6-phosphate deanimase from Stren...

ID or keywords:

Entry

Database: PDB / ID: 7kqa

Title

Crystal Structure of Glucosamine-6-phosphate deanimase from Strenotrophomonas maltophilia

Components

Iron dicitrate transport regulator FecR

Keywords

HYDROLASE / SSGCID / Glucosamine-6-phosphate deanimase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

glutamine-fructose-6-phosphate transaminase (isomerizing) / carbohydrate derivative metabolic process / carbohydrate derivative binding / transaminase activity
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 1.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Glucosamine-6-phosphate deanimase from Strenotrophomonas maltophilia
Authors: DeBouver, N.D. / Delker, S.L. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Nov 14, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7kqa.cif.gz	329.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7kqa.ent.gz	220.5 KB	Display	PDB format
PDBx/mmJSON format	7kqa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7kqa_validation.pdf.gz	458.3 KB	Display	wwPDB validaton report
Full document	7kqa_full_validation.pdf.gz	460.6 KB	Display
Data in XML	7kqa_validation.xml.gz	32.9 KB	Display
Data in CIF	7kqa_validation.cif.gz	51.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kq/7kqa ftp://data.pdbj.org/pub/pdb/validation_reports/kq/7kqa	HTTPS FTP

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Related structure data

Similar structure data	5xh9-d 3cj2-2 2a3n-1 4jso-d 5ftb-d 3p0b-d 3co9-1 2d3u-2 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: Iron dicitrate transport regulator FecR

B: Iron dicitrate transport regulator FecR

hetero molecules

74 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	57.920, 90.440, 126.720
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Iron dicitrate transport regulator FecR Mass: 36774.832 Da / Num. of mol.: 2 / Fragment: StmaA.17926.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Gene: AR275_15025, BWP19_11460 / Plasmid: StmaA.17926.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A109JTU2
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.49 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: StmaA.17926.a.B1.PW38775 [Barcode: 314016b7, PuckID: lhc5-4, Cryo: Direct, Concentration: 20 mg/mL] 170 mM Ammonium Acetate, 85 mM Sodium Citrate HCl pH 5.6, 25.5% (w/v) PEG 4000, 15% (v/v) glycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 7, 2020

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. obs: 79758 / % possible obs: 98.7 % / Redundancy: 17.001 % / B_iso Wilson estimate: 22.957 Å² / CC_1/2: 1 / R_merge(I) obs: 0.049 / R_rim(I) all: 0.05 / Χ²: 0.961 / Net I/σ(I): 38.59

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.65-1.69	5.31	0.374	3.82	5156	0.907	0.414	87.4
1.69-1.74	7.922	0.351	5.26	5464	0.949	0.376	95.2
1.74-1.79	11.084	0.293	7.77	5610	0.978	0.308	100
1.79-1.84	11.642	0.239	9.81	5435	0.987	0.25	100
1.84-1.91	12.185	0.194	12.07	5281	0.992	0.202	100
1.91-1.97	12.786	0.15	15.96	5101	0.995	0.156	100
1.97-2.05	13.379	0.121	20.09	4959	0.997	0.126	100
2.05-2.13	14.306	0.102	24.84	4752	0.998	0.106	100
2.13-2.22	17.356	0.088	33.62	4585	0.999	0.091	100
2.22-2.33	18.649	0.074	41.32	4374	0.999	0.076	100
2.33-2.46	19.707	0.067	46.66	4150	0.999	0.069	100
2.46-2.61	21.059	0.061	51.68	3952	0.999	0.063	100
2.61-2.79	23.308	0.057	59.23	3727	1	0.058	100
2.79-3.01	27.885	0.05	71.82	3495	1	0.051	100
3.01-3.3	28.59	0.042	83.1	3198	1	0.043	100
3.3-3.69	28.369	0.036	97.3	2927	1	0.036	100
3.69-4.26	28.224	0.031	107.53	2598	1	0.031	100
4.26-5.22	28.225	0.028	111.16	2222	1	0.029	100
5.22-7.38	27.903	0.029	98.88	1751	1	0.03	100
7.38-50	25.558	0.025	112.86	1021	1	0.025	99.3

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Processing

Software

Name	Version	Classification
PHENIX	1.19rc4-4035	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.27	data extraction
PARROT		phasing
PHASER		phasing
Coot		model building
PHENIX		model building
ARP/wARP		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.65→45.52 Å / SU ML: 0.1348 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.0078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1811	1985	2.49 %
R_work	0.1585	77767	-
obs	0.1591	79752	98.71 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 18.54 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→45.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4963	0	32	795	5790

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0053	5138
X-RAY DIFFRACTION	f_angle_d	0.8097	7032
X-RAY DIFFRACTION	f_chiral_restr	0.0496	826
X-RAY DIFFRACTION	f_plane_restr	0.0076	920
X-RAY DIFFRACTION	f_dihedral_angle_d	13.1088	1817

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.65-1.69	0.243	119	0.2046	4827	X-RAY DIFFRACTION	87
1.69-1.74	0.2427	143	0.182	5248	X-RAY DIFFRACTION	94.88
1.74-1.79	0.2086	142	0.1591	5582	X-RAY DIFFRACTION	99.98
1.79-1.85	0.1503	131	0.161	5580	X-RAY DIFFRACTION	100
1.85-1.91	0.2088	163	0.1754	5524	X-RAY DIFFRACTION	99.98
1.91-1.99	0.1938	135	0.1577	5590	X-RAY DIFFRACTION	100
1.99-2.08	0.1761	150	0.1538	5603	X-RAY DIFFRACTION	100
2.08-2.19	0.1927	134	0.1552	5592	X-RAY DIFFRACTION	100
2.19-2.33	0.2118	117	0.1553	5652	X-RAY DIFFRACTION	100
2.33-2.5	0.1775	148	0.1615	5603	X-RAY DIFFRACTION	100
2.51-2.76	0.1777	148	0.1668	5639	X-RAY DIFFRACTION	100
2.76-3.16	0.1871	151	0.1628	5657	X-RAY DIFFRACTION	99.97
3.16-3.98	0.1406	134	0.1451	5738	X-RAY DIFFRACTION	100
3.98-45.52	0.1788	170	0.1527	5932	X-RAY DIFFRACTION	99.9

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	0.811831703846	0.19008711448	0.570686754348	0.608227736982	0.421547178072	1.27160167863	-0.011055236928	0.0438961033279	0.0204321107255	-0.114754279071	0.0660653280597	-0.0406683084752	-0.116408532087	0.0808640810756	-0.035464257092	0.129950784346	-0.0131742270036	0.0184910094659	0.0844379074551	0.00374488482237	0.0879270560403	8.84588368408	93.825785822	7.86222243949
2	2.00176298613	-0.659870425625	0.123375622071	2.14729095521	0.432310420293	2.55082688415	-0.0141261928849	-0.199414746845	0.174765701632	-0.0382017395379	0.0420657992241	-0.0379028972654	-0.227725712445	-0.100597886052	0.00489919051367	0.130827144907	-0.0237613777633	0.00356498126055	0.105325554018	-0.00599987158903	0.106604638334	10.2803124929	104.399154044	21.331533507
3	2.62208807105	0.741244329019	2.49369824815	3.21090853687	1.53033628838	2.89163031554	-0.13438245803	-0.0398580690015	0.172396698812	-0.142311051702	0.096358421964	0.0662569728808	-0.309092363441	-0.0508129214811	0.0300438756556	0.195291704834	-0.0388559313097	0.00966749566407	0.091885037129	0.0200301272118	0.119891811842	11.2020144887	109.039911093	16.9633762303
4	2.29274840325	0.69373423686	0.220649005511	0.866114283307	0.289111783457	1.03989343068	-0.0237061122907	0.0968601698574	0.102801872652	-0.103646349608	0.0741394800799	0.00376090605557	-0.279532294115	0.101100284787	-0.0393292554278	0.192324951548	-0.0368257764068	0.0261516705106	0.102469050335	0.00126561537836	0.0822978180641	10.5848220765	98.4048815554	6.69593954309
5	6.82142042399	0.749495730774	2.24004186189	0.807819304295	0.452857600015	2.87791167161	-0.0531571905992	0.255863260057	-0.147221908982	-0.102196110137	0.0786978395974	-0.121974405942	0.049287423717	0.236656447819	-0.0401790777988	0.131684276805	-0.00132645176912	0.0417552330463	0.063047946153	-0.00674799454653	0.0645551427744	12.9901302085	82.7086111744	1.41954469021
6	2.48165991218	-0.253545141092	-1.5258551219	2.16974364701	1.25758599274	2.64656806932	-0.0546284870672	0.0142574421259	-0.241916004053	-0.0769953637982	-0.0814395884763	0.13696599729	0.027457001488	-0.205604153245	0.107036702238	0.0917558830563	-0.0171142096705	-0.00468216901073	0.0572295030863	0.0310736460191	0.131743747421	-7.22603608053	77.7902977866	14.7433469907
7	1.64167846834	0.000242311246452	0.000167986045581	1.90378068623	0.300175066516	1.18023028101	-0.0293890538091	-0.0679419474069	-0.0652377614824	0.185359360116	0.0299782348969	0.0438756561337	0.0267548135988	0.0023529283802	-0.000588692929197	0.105097323107	0.00716706077453	0.00554207722206	0.0726877226514	-0.00655385508878	0.0784970506886	-4.03041842775	82.7152155684	22.319876784
8	2.29351981808	2.14871455406	-2.47569500239	2.52637564408	-2.28277141053	3.63929310685	0.0751948302368	-0.107415567708	-0.0944169835139	0.160363668487	-0.138544814201	-0.258437671296	-0.0286739350687	0.292265700854	0.0220189785866	0.147838590264	0.0146789428279	-0.0298988885103	0.102276889664	0.00164591202958	0.158214801591	2.29928786162	71.9891217174	22.6039632067
9	2.02424157664	-0.0514733901293	0.213973926849	0.695644740199	-0.155873834896	1.18297796371	-0.0391947718587	-0.0355434309805	0.0146742967247	-0.045325157244	0.0390036350806	0.0430443843329	-0.0874053392549	-0.0844956026779	0.00170234001374	0.12333285072	-0.00422379608872	0.00180063152849	0.0814577575592	-0.000150171364572	0.0588752069678	-3.83193985397	83.7754424805	8.52886915684
10	1.13361027083	0.371783414399	-0.365235459238	0.469106922381	-0.0632238459409	1.00428347793	0.0106040743288	-0.0362680337589	-0.0140055742802	0.0754593550153	0.00048565246037	-0.0205313870017	0.0221580278983	0.0194118322747	-0.0162078976818	0.0795402439488	0.0100625618996	-0.00802790520946	0.0468582997493	0.00178185985844	0.0787233186778	6.79489554449	96.367346888	45.3419165067
11	1.90863045282	-0.117781007734	-0.743773193433	1.06885878793	-0.819032022744	2.50304170267	-0.0361551805902	0.137368453877	-0.314843664443	-0.126633026423	-0.0169917246343	-0.0812045474798	0.338870136512	0.0940690840265	0.0828016803405	0.126664238766	0.0172372856243	-0.000604661312514	0.107794347584	-0.0386558854319	0.141746612884	18.1467419332	88.4944642973	34.666132642
12	0.78274854018	0.292493655819	0.292933080957	0.469555310508	0.219644554312	0.61979642602	0.000854920827089	-0.0229325506683	0.0445569262257	0.0384993734241	-0.0394354912766	0.0563796106522	0.00966844233572	-0.022774797805	0.0659161539346	0.0849697181206	0.00957263638491	0.0121092349307	0.0684329166055	-0.00383736951566	0.0897835081775	-6.17740654869	95.4195134987	39.3579590998

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 6 through 79 )	A	A	6 - 79	1 - 74
2	2	chain 'A' and (resid 80 through 114 )	A	A	80 - 114	75 - 109
3	3	chain 'A' and (resid 115 through 135 )	A	A	115 - 135	110 - 130
4	4	chain 'A' and (resid 136 through 183 )	A	A	136 - 183	131 - 178
5	5	chain 'A' and (resid 184 through 202 )	A	A	184 - 202	179 - 197
6	6	chain 'A' and (resid 203 through 223 )	A	A	203 - 223	198 - 218
7	7	chain 'A' and (resid 224 through 270 )	A	A	224 - 270	219 - 265
8	8	chain 'A' and (resid 271 through 297 )	A	A	271 - 297	266 - 292
9	9	chain 'A' and (resid 298 through 346 )	A	A	298 - 346	293 - 341
10	10	chain 'B' and (resid 11 through 79 )	B	C	11 - 79	1 - 69
11	11	chain 'B' and (resid 80 through 135 )	B	C	80 - 135	70 - 125
12	12	chain 'B' and (resid 136 through 346 )	B	C	136 - 346	126 - 336

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