PDB-3m92: The structure of yciN, an unchracterized protein from Shigella fl...

ID or keywords:

Entry

Database: PDB / ID: 3m92

Title

The structure of yciN, an unchracterized protein from Shigella flexneri.

Components

Protein yciN

Keywords

structural genomics / unknown function / DUF2498 / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Protein of unknown function (DUF2498) / Protein of unknown function DUF2498 / YciN superfamily / Protein of unknown function (DUF2498) /

GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / Protein YciN

Function and homology information

Biological species

Shigella flexneri 2a (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.05 Å

Authors

Cuff, M.E. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of yciN, an unchracterized protein from Shigella flexneri.
Authors: Cuff, M.E. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Mar 19, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3m92.cif.gz	47.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3m92.ent.gz	34.2 KB	Display	PDB format
PDBx/mmJSON format	3m92.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/3m92 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/3m92	HTTPS FTP

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Related structure data

Similar structure data	5z7i-d 5yiw-d 5pz2-1 5pxq-1 5px5-1 5pxz-1 5pya-1 5x9o-d 5px3-1 5pwi-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc27530

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein yciN

B: Protein yciN

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	56.35, 56.35, 132.26
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Details

unknown but likely dimer in asymmetric unit.

#1: Protein	Protein yciN Mass: 12253.174 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 2457T / Gene: S1360, SF1275, yciN / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21 / References: UniProt: P0AB64
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.47 Å³/Da / Density % sol: 50.27 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.5M K3PO4, 0.5M NaPO4, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction

Mean temperature: 273 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97945, 0.97929

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2010

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	0.97929	1

Reflection

Redundancy: 12 % / Av σ(I) over netI: 50.44 / Number: 187426 / R_merge(I) obs: 0.072 / Χ²: 1.54 / D res high: 2.05 Å / D res low: 50 Å / Num. obs: 15604 / % possible obs: 97.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.56	50	87.4	1	0.068	6.917	10.2
4.42	5.56	94	1	0.057	3.987	11.4
3.86	4.42	94.8	1	0.06	3.611	11.8
3.51	3.86	96.1	1	0.066	3.197	11.9
3.25	3.51	97.1	1	0.065	2.508	12
3.06	3.25	97.2	1	0.069	1.852	12.2
2.91	3.06	97.8	1	0.072	1.339	12.1
2.78	2.91	97.9	1	0.083	1.114	12.2
2.68	2.78	98.1	1	0.094	0.885	12.1
2.58	2.68	98.2	1	0.115	0.812	12.3
2.5	2.58	99	1	0.134	0.726	12.2
2.43	2.5	98.4	1	0.162	0.656	12.2
2.37	2.43	99	1	0.189	0.602	12.2
2.31	2.37	98.5	1	0.206	0.592	12.2
2.26	2.31	99.1	1	0.24	0.563	12.3
2.21	2.26	99.3	1	0.331	0.554	12.2
2.16	2.21	98.9	1	0.376	0.554	12
2.12	2.16	99.2	1	0.483	0.497	12.4
2.09	2.12	99.4	1	0.643	0.487	12.1
2.05	2.09	99.5	1	0.655	0.476	12.3

Reflection

Resolution: 2.05→50 Å / Num. all: 15604 / Num. obs: 15604 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / B_iso Wilson estimate: 46.3 Å² / R_merge(I) obs: 0.072 / Χ²: 1.541 / Net I/σ(I): 9.5

Reflection shell

Resolution: 2.05→2.09 Å / Redundancy: 12.3 % / R_merge(I) obs: 0.655 / Num. unique all: 791 / Χ²: 0.476 / % possible all: 99.5

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.05 Å / D res low: 48.8 Å / FOM : 0.301 / FOM acentric: 0.32 / FOM centric: 0.176 / Reflection: 15536 / Reflection acentric: 13472 / Reflection centric: 2064

Phasing MAD set

Highest resolution: 2.05 Å / Lowest resolution: 48.8 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.63	1	0	0	0	0	13472	2064
2	0.98	0.95	9	13.4	0.39	0.33	12543	1976

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	12.67-48.8	1.49	1	0.3	0.1	0	0	32	29
1	7.28-12.67	1.03	1	0.2	0.2	0	0	196	88
1	5.11-7.28	1.55	1	0.2	0.1	0	0	509	163
1	3.93-5.11	1.17	1	0.1	0.1	0	0	1001	208
1	3.2-3.93	1.26	1	0.1	0	0	0	1614	288
1	2.7-3.2	2.35	1	0	0	0	0	2386	354
1	2.33-2.7	10.56	1	0	0	0	0	3321	419
1	2.05-2.33	3.13	1	0	0	0	0	4413	515
2	12.67-48.8	1.07	1	22.3	22.5	0.96	0.95	32	29
2	7.28-12.67	0.97	0.92	25.1	28.8	0.68	0.52	196	88
2	5.11-7.28	0.93	0.91	15	17.9	0.92	0.69	509	163
2	3.93-5.11	0.96	0.93	19	22.2	0.47	0.36	1001	208
2	3.2-3.93	0.99	0.96	16.5	20.7	0.33	0.23	1614	288
2	2.7-3.2	0.98	0.97	9.4	13.1	0.32	0.19	2386	354
2	2.33-2.7	0.98	0.98	5.4	6.9	0.29	0.18	3320	419
2	2.05-2.33	0.99	1	3.8	5.2	0.21	0.12	3485	427

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	63.4469	-0.195	-0.86	-0.009	4.779	0
2	66.7653	-0.205	-0.798	0.046	4.894	0
3	68.4683	-0.322	-0.707	-0.138	1.114	0
4	56.8645	-0.194	-0.858	-0.009	2.609	-0.21
5	62.1972	-0.204	-0.797	0.046	2.669	-0.237
6	61.387	-0.327	-0.711	-0.137	0.505	-0.038

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.67-48.8	0.517	0.626	0.396	61	32	29
7.28-12.67	0.486	0.574	0.29	284	196	88
5.11-7.28	0.614	0.679	0.412	672	509	163
3.93-5.11	0.52	0.575	0.254	1209	1001	208
3.2-3.93	0.46	0.507	0.197	1902	1614	288
2.7-3.2	0.41	0.444	0.185	2740	2386	354
2.33-2.7	0.258	0.273	0.132	3740	3321	419
2.05-2.33	0.102	0.108	0.054	4928	4413	515

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 15536

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
6.45-100	57	0.769	502
5.12-6.45	54.6	0.89	503
4.48-5.12	55.1	0.917	506
4.07-4.48	58.6	0.904	504
3.77-4.07	61.9	0.916	506
3.55-3.77	63.2	0.905	503
3.37-3.55	59.2	0.907	508
3.22-3.37	60.8	0.893	511
3.09-3.22	61.8	0.892	516
2.98-3.09	59.3	0.891	536
2.88-2.98	58.6	0.882	548
2.79-2.88	60.6	0.865	568
2.7-2.79	62.5	0.882	597
2.63-2.7	65.3	0.866	631
2.56-2.63	66.2	0.869	603
2.49-2.56	67.9	0.87	659
2.43-2.49	70.4	0.856	642
2.37-2.43	71.5	0.878	687
2.32-2.37	69.3	0.886	682
2.27-2.32	74.4	0.886	717
2.23-2.27	74.9	0.881	714
2.18-2.23	77	0.894	741
2.14-2.18	81.4	0.894	750
2.1-2.14	82.2	0.877	753
2.05-2.1	86.6	0.838	1149

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	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: 2.05→28.18 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.946 / WR_factor R_free: 0.248 / WR_factor R_work: 0.203 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.864 / SU B: 8.851 / SU ML: 0.11 / SU R Cruickshank DPI: 0.16 / SU R_free: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.154
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	0.241	769	4.9 %	RANDOM
R_work	0.198	-	-	-
all	0.2	15541	-	-
obs	0.2	15541	97.62 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 63.14 Å² / B_iso mean: 35.166 Å² / B_iso min: 13.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0.03 Å²	0 Å²
2-	-	0.06 Å²	0 Å²
3-	-	-	-0.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→28.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1253	0	2	91	1346

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	1311
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	856
X-RAY DIFFRACTION	r_angle_refined_deg	1.394	1.955	1783
X-RAY DIFFRACTION	r_angle_other_deg	0.923	3	2110
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.379	5	169
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.358	24.839	62
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.185	15	230
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.157	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	211
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1462
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	256
X-RAY DIFFRACTION	r_mcbond_it	0.879	1.5	812
X-RAY DIFFRACTION	r_mcbond_other	0.21	1.5	331
X-RAY DIFFRACTION	r_mcangle_it	1.704	2	1313
X-RAY DIFFRACTION	r_scbond_it	2.862	3	499
X-RAY DIFFRACTION	r_scangle_it	4.645	4.5	465

LS refinement shell

Resolution: 2.05→2.103 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	61	-
R_work	0.226	1077	-
all	-	1138	-
obs	-	-	99.3 %

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	2.2215	0.6935	-0.3794	2.1921	-0.4361	2.1884	0.0832	-0.0773	0.0453	0.1897	-0.1379	-0.167	-0.1254	0.1904	0.0547	0.172	-0.1031	-0.0491	0.0719	0.0435	0.1409	40.0982	14.7199	1.8222
2	2.4245	0.4812	-0.068	2.3921	-1.2259	2.732	-0.0263	-0.0573	-0.1004	0.0564	-0.0569	-0.1294	0.0552	0.0219	0.0832	0.1448	-0.0874	-0.0375	0.0573	0.0398	0.1628	34.8391	5.5072	1.7302

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 82
2	X-RAY DIFFRACTION	1	A	86
3	X-RAY DIFFRACTION	1	A	87 - 125
4	X-RAY DIFFRACTION	2	B	2 - 82
5	X-RAY DIFFRACTION	2	B	86
6	X-RAY DIFFRACTION	2	B	87 - 138

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