PDB-7rhe: Crystal Structure of ROK family protein from Burkholderia vietnam...

ID or keywords:

Entry

Database: PDB / ID: 7rhe

Title

Crystal Structure of ROK family protein from Burkholderia vietnamiensis G4

Components

ROK family protein

Keywords

TRANSCRIPTION / SSGCID / NagC/XylR / Bcep1808_1509 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

N-acylmannosamine kinase activity / N-acetylneuraminate catabolic process
Similarity search - Function

Biological species

Burkholderia vietnamiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of ROK family protein from Burkholderia vietnamiensis G4
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jul 16, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7rhe.cif.gz	179 KB	Display	PDBx/mmCIF format
PDB format	pdb7rhe.ent.gz	118.4 KB	Display	PDB format
PDBx/mmJSON format	7rhe.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7rhe_validation.pdf.gz	416.8 KB	Display	wwPDB validaton report
Full document	7rhe_full_validation.pdf.gz	419.7 KB	Display
Data in XML	7rhe_validation.xml.gz	14.8 KB	Display
Data in CIF	7rhe_validation.cif.gz	20.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rh/7rhe ftp://data.pdbj.org/pub/pdb/validation_reports/rh/7rhe	HTTPS FTP

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Related structure data

Similar structure data	5jk6-d 1mkf-d 5jk8-d 2w00-2 4bec-1 6h2j-1 2qez-4 4bec-2 4het-d 3qr0-d 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

Deposited unit

A: ROK family protein

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

1

A: ROK family protein

defined by author&software
Evidence: gel filtration
90.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	112.410, 112.410, 63.090
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-571- HOH

#1: Protein	ROK family protein Mass: 45044.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria) Strain: G4 / LMG 22486 / Gene: Bcep1808_1509 / Plasmid: BuviA.12797.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4JE13
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

ROK family protein

Mass: 45044.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_1509 / Plasmid: BuviA.12797.a.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4JE13

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.56 Å³/Da / Density % sol: 52.1 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: RigakuReagents JCSG+ screen, condition H7: 200mM ammonium sulfate, 100mM BisTris pH 5.5, 25% (w/V) PEG 3350: BuviA.12797.a.B1.PS02541 at 19.5mg/ml + 2mM ADP 4mM glucose + 2mM MgCl2': tray ...Details: RigakuReagents JCSG+ screen, condition H7: 200mM ammonium sulfate, 100mM BisTris pH 5.5, 25% (w/V) PEG 3350: BuviA.12797.a.B1.PS02541 at 19.5mg/ml + 2mM ADP 4mM glucose + 2mM MgCl2': tray 269309 h7: cryio: 20% EG: puck: ocr0-5

Crystal

Density Matthews: 2.56 Å³/Da / Density % sol: 52.1 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: RigakuReagents JCSG+ screen, condition H7: 200mM ammonium sulfate, 100mM BisTris pH 5.5, 25% (w/V) PEG 3350: BuviA.12797.a.B1.PS02541 at 19.5mg/ml + 2mM ADP 4mM glucose + 2mM MgCl2': tray ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 3, 2016 / Details: Beryllium Lenses

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 20667 / % possible obs: 99.6 % / Redundancy: 8.413 % / B_iso Wilson estimate: 55.337 Å² / CC_1/2: 1 / R_merge(I) obs: 0.054 / R_rim(I) all: 0.057 / Χ²: 1.025 / Net I/σ(I): 24.05

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
2.3-2.36	8.497	0.578	3.79	1514	0.911	0.616	100
2.36-2.42	8.461	0.488	4.42	1480	0.936	0.519	100
2.42-2.49	8.577	0.385	5.61	1441	0.954	0.409	99.9
2.49-2.57	8.52	0.326	6.57	1387	0.967	0.348	100
2.57-2.66	8.506	0.258	7.91	1347	0.978	0.275	100
2.66-2.75	8.486	0.193	10.61	1327	0.987	0.205	99.8
2.75-2.85	8.508	0.152	13.17	1262	0.992	0.162	100
2.85-2.97	8.496	0.113	16.68	1227	0.995	0.12	99.9
2.97-3.1	8.515	0.096	19.72	1163	0.996	0.102	99.9
3.1-3.25	8.438	0.075	24.63	1120	0.998	0.08	99.8
3.25-3.43	8.477	0.057	31.37	1057	0.998	0.06	99.6
3.43-3.64	8.388	0.048	37.85	1019	0.999	0.052	99.7
3.64-3.89	8.341	0.041	42.82	956	0.999	0.043	99.6
3.89-4.2	8.29	0.037	48.4	890	0.999	0.039	99.4
4.2-4.6	8.295	0.034	54.32	816	0.999	0.036	99.1
4.6-5.14	8.229	0.032	56.46	757	0.999	0.034	99.5
5.14-5.94	8.246	0.03	54.75	642	0.999	0.032	98.5
5.94-7.27	8.163	0.026	57.02	566	1	0.028	98.6
7.27-10.29	8.007	0.02	65.07	448	1	0.021	98.5
10.29-50	6.948	0.019	63.78	248	0.999	0.021	91.5

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: ab-initio model from RobeTTA-fold

Resolution: 2.3→48.67 Å / SU ML: 0.2775 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.249	2184	10.57 %	0
R_work	0.1993	18478	-	-
obs	0.2047	20662	99.69 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 62.6 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→48.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2660	0	0	76	2736

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0061	2710
X-RAY DIFFRACTION	f_angle_d	0.8155	3703
X-RAY DIFFRACTION	f_chiral_restr	0.0502	438
X-RAY DIFFRACTION	f_plane_restr	0.0074	492
X-RAY DIFFRACTION	f_dihedral_angle_d	13.4251	947

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 (%)
2.3-2.35	0.3601	146	0.2854	1142	X-RAY DIFFRACTION	100
2.35-2.4	0.2764	139	0.2625	1122	X-RAY DIFFRACTION	100
2.4-2.46	0.3175	140	0.2528	1147	X-RAY DIFFRACTION	99.92
2.46-2.53	0.2823	129	0.2297	1164	X-RAY DIFFRACTION	100
2.53-2.61	0.2708	140	0.2374	1125	X-RAY DIFFRACTION	100
2.61-2.69	0.2814	137	0.2342	1157	X-RAY DIFFRACTION	100
2.69-2.79	0.2908	113	0.2292	1152	X-RAY DIFFRACTION	99.84
2.79-2.9	0.2784	157	0.2353	1126	X-RAY DIFFRACTION	99.84
2.9-3.03	0.2579	121	0.2265	1169	X-RAY DIFFRACTION	99.92
3.03-3.19	0.3001	122	0.2185	1178	X-RAY DIFFRACTION	99.92
3.19-3.39	0.2788	161	0.2262	1136	X-RAY DIFFRACTION	99.85
3.39-3.65	0.2549	142	0.2001	1130	X-RAY DIFFRACTION	99.69
3.65-4.02	0.222	133	0.1826	1180	X-RAY DIFFRACTION	99.55
4.02-4.6	0.2	129	0.1624	1163	X-RAY DIFFRACTION	99.46
4.6-5.79	0.2304	145	0.1883	1166	X-RAY DIFFRACTION	99.09
5.8-48.67	0.2237	130	0.1689	1221	X-RAY DIFFRACTION	98.04

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	2.5398633673	-0.429809115275	0.747046917647	0.120123558326	-0.0158984973193	0.581321281791	0.181591667091	0.0925272690448	0.926562372197	-0.234722713832	0.661288363891	-0.43704629858	-0.386597170683	0.198406227632	-0.737377383492	0.683578325603	-0.153881329404	0.249365329465	0.702169199257	-0.0614343364283	2.11170560286	58.1764635237	81.2626737671	24.661052227
2	4.0435857109	-0.431292023665	-1.41864349248	4.10680591136	2.67235202213	5.00429217674	0.212196242348	0.406956635178	0.223742164662	-0.139107203664	-0.155999260427	0.353595216373	0.0995430171739	-0.348113131784	-0.0129216187056	0.310422309688	-0.00047297102064	0.033873760394	0.348013752082	0.0404886609431	0.48462643329	51.3834105062	55.6864366787	14.1350024489
3	4.69378380005	0.622378365673	-0.657540079849	2.20625305869	0.408314181261	3.1744234932	-0.0704246577211	-0.331494151226	-0.486656930489	0.417982635174	-0.0679331605	0.440808717689	0.544842499625	-0.143062031535	0.0576648910771	0.377232097244	-0.0360907456218	0.0694824796396	0.26948159514	0.0237959042276	0.373193103194	71.8434858224	45.9337488883	17.3401654226
4	7.36136066385	-0.497116569275	-0.330230640956	2.89176078409	0.201554094031	4.04026344442	-0.129767901658	-0.41528576451	0.044193517851	0.531145121466	0.0581264719281	0.157487402671	0.239548601142	-0.102057733224	0.0703860734172	0.492293722382	-0.0655397532294	0.11039004959	0.354128276535	-0.0283792909937	0.306138776143	70.6337560532	54.8109847068	24.1158030053

Refinement TLS group

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

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 14 through 58 )	14 - 58	1 - 45
2	2	chain 'A' and (resid 59 through 209 )	59 - 209	46 - 186
3	3	chain 'A' and (resid 210 through 330 )	210 - 330	187 - 307
4	4	chain 'A' and (resid 331 through 391 )	331 - 391	308 - 368

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