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- PDB-3h36: Structure of an uncharacterized domain in polyribonucleotide nucl... -

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Open data

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Basic information

Entry

Database: PDB / ID: 3h36

Title

Structure of an uncharacterized domain in polyribonucleotide nucleotidyltransferase from Streptococcus mutans UA159

Components

Polyribonucleotide nucleotidyltransferase

Keywords

TRANSFERASE / Streptococcus mutans / polyribonucleotide nucleotidyltransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Nucleotidyltransferase / RNA-binding

Function / homology

Function and homology information

polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / mRNA catabolic process / RNA processing / magnesium ion binding / RNA binding / cytoplasm
Similarity search - Function

Biological species

Streptococcus mutans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Cuff, M.E. / Hatzos, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Structure of an uncharacterized domain in polyribonucleotide nucleotidyltransferase from Streptococcus mutans UA159
Authors: Cuff, M.E. / Hatzos, C. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Apr 15, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 12, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	3h36.cif.gz	31.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3h36.ent.gz	22.4 KB	Display	PDB format
PDBx/mmJSON format	3h36.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3h36_validation.pdf.gz	427.6 KB	Display	wwPDB validaton report
Full document	3h36_full_validation.pdf.gz	427.9 KB	Display
Data in XML	3h36_validation.xml.gz	6.6 KB	Display
Data in CIF	3h36_validation.cif.gz	8.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h3/3h36 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/3h36	HTTPS FTP

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Related structure data

Similar structure data	3o7i-2 2fi1-d 6gz1-d 6dkq-d 5elj-d 6uxo-2 5t9p-6 4db9-5 4db9-3 6uxo-3 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: apc63929.2

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#86 - Feb 2007 Exosomes similarity (10) #253 - Jan 2021 Expressome similarity (5) #255 - Mar 2021 Cisplatin and DNA similarity (4) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

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Assembly

Deposited unit

A: Polyribonucleotide nucleotidyltransferase

hetero molecules

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

1

A: Polyribonucleotide nucleotidyltransferase

hetero molecules

A: Polyribonucleotide nucleotidyltransferase

hetero molecules

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

2

A: Polyribonucleotide nucleotidyltransferase

hetero molecules

A: Polyribonucleotide nucleotidyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.312, 59.312, 93.090
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

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Components

#1: Protein	Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / PNPase / 1.10.10.400.hmm mega family domain Mass: 10867.694 Da / Num. of mol.: 1 / Fragment: residues 231-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: pnp, pnpA, SMU_155 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q8DWB2, polyribonucleotide nucleotidyltransferase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	AUTHORS STATE THAT THE ELECTRON DENSITY MAPS IN THIS REGION ARE OF A HIGH QUALITY AND CLEARLY SHOW ...AUTHORS STATE THAT THE ELECTRON DENSITY MAPS IN THIS REGION ARE OF A HIGH QUALITY AND CLEARLY SHOW A SERINE IN THIS POSITION. THE HYDROGEN-BONDING PATTERN AROUND THE OG OF SER 264 IS ALSO CONSISTENT WITH THIS IDENTIFICATION. ARG AND SER CODONS DIFFER ONLY BY THE LAST BASE PAIR. AUTHORS ARE NOT SURE ABOUT WHETHER THIS DIFFERENCE OCCURRED DURING SEQUENCING OR CLONING.

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.44 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Na Cacodylate pH6.5,0.2M Ca Acetate, 40% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97945,0.97931

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2009

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97945	1
2	0.97931	1

Reflection

Redundancy: 11.9 % / Av σ(I) over netI: 65.5 / Number: 255616 / R_merge(I) obs: 0.08 / Χ²: 2.54 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 21470 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.61	50	97.3	1	0.071	8.885	10.7
3.66	4.61	100	1	0.056	5.621	11.4
3.2	3.66	100	1	0.075	5.654	11.7
2.91	3.2	100	1	0.079	4.258	11.8
2.7	2.91	100	1	0.092	4.092	12
2.54	2.7	100	1	0.09	3.117	12
2.41	2.54	100	1	0.086	2.44	12
2.31	2.41	100	1	0.089	2.077	12
2.22	2.31	100	1	0.098	1.945	12.1
2.14	2.22	100	1	0.111	1.644	12.2
2.07	2.14	100	1	0.115	1.383	12
2.02	2.07	100	1	0.14	1.422	12.1
1.96	2.02	100	1	0.166	1.212	12.1
1.91	1.96	100	1	0.213	1.146	12.2
1.87	1.91	100	1	0.254	1.057	12
1.83	1.87	100	1	0.293	1.033	12.1
1.79	1.83	100	1	0.37	1.024	12.2
1.76	1.79	100	1	0.47	0.992	11.9
1.73	1.76	100	1	0.56	1.003	12.1
1.7	1.73	100	1	0.657	0.979	11.5

Reflection

Resolution: 1.7→50 Å / Num. all: 11267 / Num. obs: 11267 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 22.7 % / B_iso Wilson estimate: 28.2 Å² / R_merge(I) obs: 0.082 / Χ²: 2.246 / Net I/σ(I): 65.5

Reflection shell

Resolution: 1.7→1.73 Å / Redundancy: 22.4 % / R_merge(I) obs: 0.671 / Num. unique all: 541 / Χ²: 0.824 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.7 Å / D res low: 50 Å / FOM : 0.521 / FOM acentric: 0.552 / FOM centric: 0.4 / Reflection: 11202 / Reflection acentric: 8939 / Reflection centric: 2263

Phasing MAD set

Highest resolution: 1.7 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.6	1	0.2	0.2	0	0	8939	2263
2	0.83	0.7	3	4.7	1.01	0.94	8935	2262

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	10.99-50	1.33	1	0.7	0.4	0	0	14	38
1	6.17-10.99	1.21	1	0.6	0.4	0	0	117	108
1	4.29-6.17	1.45	1	0.6	0.4	0	0	326	177
1	3.29-4.29	1.28	1	0.4	0.3	0	0	640	257
1	2.67-3.29	1.55	1	0.3	0.2	0	0	1064	318
1	2.24-2.67	1.71	1	0.2	0.1	0	0	1591	389
1	1.93-2.24	1.93	1	0.1	0	0	0	2222	452
1	1.7-1.93	2.72	1	0.1	0	0	0	2965	524
2	10.99-50	0.74	0.54	8.7	7.8	1.81	1.97	14	37
2	6.17-10.99	0.88	0.7	9	10.1	1.59	1.31	116	108
2	4.29-6.17	0.75	0.55	6	7.7	1.81	1.45	326	177
2	3.29-4.29	0.66	0.6	4.4	5.5	1.81	1.32	640	257
2	2.67-3.29	0.75	0.65	3.7	4.7	1.37	1.06	1064	318
2	2.24-2.67	0.79	0.71	2.5	3.5	1.22	0.92	1591	389
2	1.93-2.24	0.9	0.81	2.4	3.5	0.72	0.54	2222	452
2	1.7-1.93	0.98	0.96	2.6	4	0.36	0.25	2962	524

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	32.41669	0.588	0.593	0.01	0
2	Se	41.62799	0.825	0.74	-0.056	0
3	Se	34.78328	0.589	0.593	0.011	-0.132
4	Se	39.02891	0.825	0.74	-0.056	-0.114

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10.99-50	0.574	0.593	0.567	52	14	38
6.17-10.99	0.568	0.682	0.445	225	117	108
4.29-6.17	0.684	0.771	0.523	503	326	177
3.29-4.29	0.755	0.814	0.609	897	640	257
2.67-3.29	0.725	0.781	0.538	1382	1064	318
2.24-2.67	0.69	0.74	0.484	1980	1591	389
1.93-2.24	0.515	0.552	0.331	2674	2222	452
1.7-1.93	0.262	0.282	0.147	3489	2965	524

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 11202

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.01-100	46.9	0.803	503
3.93-5.01	38.3	0.926	502
3.41-3.93	41.8	0.92	508
3.08-3.41	38.2	0.919	502
2.85-3.08	40.2	0.915	505
2.68-2.85	40.1	0.905	501
2.54-2.68	36.5	0.902	501
2.42-2.54	36.6	0.912	514
2.32-2.42	40.3	0.909	514
2.24-2.32	41.6	0.905	507
2.16-2.24	43.9	0.881	507
2.1-2.16	46.7	0.873	506
2.04-2.1	50.4	0.88	507
1.99-2.04	49.5	0.869	508
1.94-1.99	59.3	0.851	513
1.9-1.94	57	0.832	501
1.86-1.9	60.9	0.816	502
1.82-1.86	68.8	0.816	524
1.79-1.82	65.7	0.804	522
1.76-1.79	68.8	0.827	529
1.7-1.76	73.4	0.735	1026

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Processing

Software

Name	Version	Classification	NB
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.8→44.99 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.932 / WR_factor R_free: 0.237 / WR_factor R_work: 0.213 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.908 / SU B: 5.494 / SU ML: 0.08 / SU R Cruickshank DPI: 0.139 / SU R_free: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.236	460	4.8 %	RANDOM
R_work	0.199	-	-	-
all	0.201	9492	-	-
obs	0.201	9492	99.78 %	-

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 max: 73.28 Å² / B_iso mean: 25.85 Å² / B_iso min: 13.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.36 Å²	0.68 Å²	0 Å²
2-	-	1.36 Å²	0 Å²
3-	-	-	-2.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→44.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	633	0	5	90	728

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.021	703
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	477
X-RAY DIFFRACTION	r_angle_refined_deg	1.538	1.95	951
X-RAY DIFFRACTION	r_angle_other_deg	0.956	3	1170
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.515	5	89
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.158	25.476	42
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.808	15	139
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.032	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	103
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	817
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	133
X-RAY DIFFRACTION	r_mcbond_it	0.869	1.5	424
X-RAY DIFFRACTION	r_mcbond_other	0.258	1.5	168
X-RAY DIFFRACTION	r_mcangle_it	1.822	2	687
X-RAY DIFFRACTION	r_scbond_it	3.357	3	279
X-RAY DIFFRACTION	r_scangle_it	5.846	4.5	264

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.359	30	-
R_work	0.197	649	-
all	-	679	-
obs	-	-	99.85 %

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	1.3576	-0.2899	0.0403	1.5531	1.3996	5.9805	0.1187	0.2564	-0.0536	-0.0812	0.011	0.0112	-0.013	0.2179	-0.1297	0.0223	0.0168	-0.022	0.058	-0.0069	0.0335	21.3691	33.4464	3.4772
2	6.2109	2.0805	-2.3431	2.9048	-1.5834	9.4842	-0.0571	0.3231	0.1017	-0.3331	0.0817	0.3654	-0.0226	-0.4527	-0.0246	0.0483	0.0078	-0.0508	0.034	-0.0051	0.0538	15.5087	35.0532	-1.8874

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	227 - 287
2	X-RAY DIFFRACTION	2	A	288 - 320

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