PDB-7k47: Crystal Structure of Glucosamine-1-phosphate N-acetyltransferase ...

ID or keywords:

Entry

Database: PDB / ID: 7k47

Title

Crystal Structure of Glucosamine-1-phosphate N-acetyltransferase from Stenotrophomonas maltophilia K279a

Components

Bifunctional protein GlmU

Keywords

TRANSFERASE / SSGCID / N-acetylglucosamine-1-phosphate uridyltransferase / Glucosamine-1-phosphate N-acetyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape ...
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Glucosamine-1-phosphate N-acetyltransferase from Stenotrophomonas maltophilia K279a
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Sep 14, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 23, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7k47.cif.gz	216.8 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	7k47.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7k47_validation.pdf.gz	421.5 KB	Display	wwPDB validaton report
Full document	7k47_full_validation.pdf.gz	425.8 KB	Display
Data in XML	7k47_validation.xml.gz	17.4 KB	Display
Data in CIF	7k47_validation.cif.gz	23.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k4/7k47 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/7k47	HTTPS FTP

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Related structure data

Related structure data	5vmkS S: Starting model for refinement
Similar structure data	4kpz-1 2vd4-1 1g97-1 4kpx-1 2v0j-1 1hm0-1 4kql-1 1hm0-2 2v0l-1 4knr-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (4) #49 - Jan 2004 Carbonic Anhydrase similarity (4) #39 - Mar 2003 lac Repressor similarity (3) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: Bifunctional protein GlmU

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

1

A: Bifunctional protein GlmU

defined by author&software
Evidence: gel filtration
148 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.290, 91.290, 184.550
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃
Space group name Hall	P6c
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/2 #3: y,-x+y,z+1/2 #4: -y,x-y,z #5: -x+y,-x,z #6: -x,-y,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-524- HOH

#1: Protein	Bifunctional protein GlmU / StmaA.00150.a.B1 Mass: 49201.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: glmU, Smlt4108 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B2FHY5, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Bifunctional protein GlmU / StmaA.00150.a.B1

Mass: 49201.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: glmU, Smlt4108 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B2FHY5, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 40 / 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: 4.52 Å³/Da / Density % sol: 72.8 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Optimization screen based on Rigaku Reagens JCSG+ condition B4: 100mM HEPES free acid / Sodium hydroxide pH 8.0, 8% (V/V) ethylene glycol, 9.6% (w/V) PEG 8000: StmaA.00150.a.B1.PW38698 at ...Details: Optimization screen based on Rigaku Reagens JCSG+ condition B4: 100mM HEPES free acid / Sodium hydroxide pH 8.0, 8% (V/V) ethylene glycol, 9.6% (w/V) PEG 8000: StmaA.00150.a.B1.PW38698 at 24mg/ml: tray 319930h10: cryo: 20% EG in 2 steps: puck aod1-6

Crystal

Density Matthews: 4.52 Å³/Da / Density % sol: 72.8 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Optimization screen based on Rigaku Reagens JCSG+ condition B4: 100mM HEPES free acid / Sodium hydroxide pH 8.0, 8% (V/V) ethylene glycol, 9.6% (w/V) PEG 8000: StmaA.00150.a.B1.PW38698 at ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 16, 2020 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.9→50 Å / Num. obs: 19333 / % possible obs: 99.9 % / Redundancy: 11.482 % / B_iso Wilson estimate: 79.637 Å² / CC_1/2: 1 / R_merge(I) obs: 0.051 / R_rim(I) all: 0.054 / Χ²: 0.945 / Net I/σ(I): 30.57

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
2.9-2.98	11.585	0.543	4.83	1433	0.947	0.568	100
2.98-3.06	11.592	0.402	6.34	1394	0.977	0.42	100
3.06-3.15	11.606	0.295	8.83	1356	0.986	0.309	100
3.15-3.24	11.587	0.218	11.59	1308	0.991	0.228	100
3.24-3.35	11.594	0.172	14.62	1257	0.994	0.179	100
3.35-3.47	11.567	0.118	19.48	1233	0.997	0.124	100
3.47-3.6	11.582	0.085	25.21	1194	0.999	0.089	100
3.6-3.74	11.562	0.07	29.75	1143	0.999	0.073	100
3.74-3.91	11.533	0.059	34.68	1088	0.999	0.062	100
3.91-4.1	11.542	0.05	39.57	1065	0.999	0.053	100
4.1-4.32	11.522	0.043	44.56	994	0.999	0.045	100
4.32-4.59	11.512	0.037	48.61	951	1	0.039	99.8
4.59-4.9	11.509	0.035	50.72	872	0.999	0.037	99.2
4.9-5.29	11.419	0.037	51.78	829	1	0.039	99.9
5.29-5.8	11.429	0.039	52.92	763	0.999	0.041	100
5.8-6.48	11.386	0.039	53.83	694	0.999	0.041	100
6.48-7.49	11.285	0.037	58.26	608	0.999	0.038	99.8
7.49-9.17	11.184	0.033	62.91	522	1	0.035	100
9.17-12.97	10.842	0.033	64.7	406	1	0.035	100
12.97-50	8.91	0.037	52.9	223	0.999	0.04	95.7

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.18.2	refinement
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: two domains of PDB entry 5vmk as per Morda

5vmk

Resolution: 2.9→29.88 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2054	1982	10.31 %	0
R_work	0.1741	17250	-	-
obs	0.1774	19232	99.65 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 95.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→29.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3285	0	0	40	3325

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3340
X-RAY DIFFRACTION	f_angle_d	0.6101	4568
X-RAY DIFFRACTION	f_chiral_restr	0.047	546
X-RAY DIFFRACTION	f_plane_restr	0.0044	609
X-RAY DIFFRACTION	f_dihedral_angle_d	18.5393	1165

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 (%)
2.9-2.97	0.3545	134	0.2642	1240	X-RAY DIFFRACTION	99.93
2.97-3.05	0.2922	148	0.2573	1231	X-RAY DIFFRACTION	100
3.05-3.14	0.2941	159	0.2439	1219	X-RAY DIFFRACTION	100
3.14-3.24	0.3189	129	0.2562	1243	X-RAY DIFFRACTION	100
3.24-3.36	0.2728	145	0.25	1220	X-RAY DIFFRACTION	100
3.36-3.49	0.2346	144	0.2212	1239	X-RAY DIFFRACTION	100
3.49-3.65	0.2255	122	0.1901	1252	X-RAY DIFFRACTION	99.93
3.65-3.84	0.2406	142	0.1914	1229	X-RAY DIFFRACTION	99.93
3.84-4.08	0.2046	161	0.1664	1197	X-RAY DIFFRACTION	100
4.09-4.4	0.1732	145	0.1522	1250	X-RAY DIFFRACTION	99.93
4.4-4.84	0.1632	129	0.1428	1224	X-RAY DIFFRACTION	98.4
4.84-5.54	0.1919	172	0.1545	1194	X-RAY DIFFRACTION	99.42
5.54-6.96	0.2081	116	0.1782	1272	X-RAY DIFFRACTION	99.93
6.96-29.88	0.1564	136	0.1334	1240	X-RAY DIFFRACTION	98.08

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	7.03895279707	-2.75034165227	-4.60254664858	2.77292957652	0.947251642586	6.98630388387	0.106648672309	1.00911032151	0.238530852284	-0.524687212164	-0.325054719763	0.422491891783	-0.132713950739	-1.16227651483	0.132842018201	0.526753766109	0.151889039368	-0.134536356812	0.800129387709	-0.0459068268756	0.751488406089	21.5069325332	42.0491017612	31.4803558452
2	1.67354359766	-2.23643233551	-1.41530733323	3.3506561399	1.33798879276	1.96696427482	0.424248207485	1.19871247256	0.358228213256	-0.803649512187	-0.444947100583	0.697270749428	-0.551723982298	-1.18802322973	-0.0222323425526	0.633845621971	0.36005800887	-0.158435612948	1.3423073852	0.0293056833638	1.0957520107	16.8978038016	49.0907569274	28.591827664
3	6.07278429508	-0.229597662057	-5.30407487434	7.14093825197	1.03464911817	8.89703917188	-0.0933100229856	-0.0327557981099	-0.0645520531646	0.514217947227	-0.249163233652	0.721151682049	0.104198503115	-0.204397065421	0.192779285155	0.452673924311	0.075188779445	0.0171422221805	0.720129447355	-0.0679394875866	0.695678080859	19.9111096338	40.902764377	42.8811741203
4	6.72998620627	0.983882774472	0.562894935468	5.02982004948	1.0216674613	2.60058013446	0.489269865357	-2.10103754631	0.0956679902027	1.60903209946	0.415399467107	-0.443837281901	-0.800797492276	2.31210107706	-0.671757070666	1.07729134497	0.0714552548135	0.0256725882579	1.7798636548	-0.0755442354319	0.778849505157	29.1991024867	42.4465664861	55.477963017
5	2.91538269635	-1.57077682496	-2.04849399648	1.36660529721	1.308615089	3.10355190558	-0.212706197856	-0.682860343883	0.441245047266	0.504073410415	0.311960088351	0.179758344168	-0.178824519594	0.125768414522	-0.0852710696645	0.757793052583	0.176862352593	0.0462944879099	0.872520250742	-0.0767058524491	0.902298823676	24.5238426028	41.7380872251	43.0926215453
6	1.94753312721	-0.0111138127477	-0.0920539883393	1.75476594941	-0.150010974175	3.92203256614	0.0101928327851	0.749879998525	-0.17663457446	-0.774451051506	0.0174225303003	0.251978720041	0.279622500466	-0.454399211397	-0.0234335112512	0.743673989278	-0.0366720895895	-0.124016218325	0.737417474668	-0.0435507910784	0.506083230407	35.3863493831	21.0909439959	-2.34210215746

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: BA2 / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -1 through 45 )	-1 - 45	1 - 47
2	2	chain 'A' and (resid 46 through 81 )	46 - 81	48 - 83
3	3	chain 'A' and (resid 82 through 138 )	82 - 138	84 - 140
4	4	chain 'A' and (resid 139 through 171 )	139 - 171	141 - 173
5	5	chain 'A' and (resid 172 through 249 )	172 - 249	174 - 251
6	6	chain 'A' and (resid 250 through 453 )	250 - 453	252 - 455

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