PDB-3qvo: Structure of a Rossmann-fold NAD(P)-binding family protein from S...

ID or keywords:

Entry

Database: PDB / ID: 3qvo

Title

Structure of a Rossmann-fold NAD(P)-binding family protein from Shigella flexneri.

Components

NmrA family protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 5-MERCAPTO-2-NITRO-BENZOIC ACID / :

Function and homology information

Biological species

Shigella flexneri 2a (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

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

Citation

Journal: TO BE PUBLISHED
Title: Structure of a Rossmann-fold NAD(P)-binding family protein from Shigella flexneri.
Authors: Cuff, M.E. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, A.

History

Deposition	Feb 25, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 1, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 3, 2018	Group: Data collection Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_source / reflns_shell Item: _reflns_shell.pdbx_diffrn_id
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qvo.cif.gz	99 KB	Display	PDBx/mmCIF format
PDB format	pdb3qvo.ent.gz	72.7 KB	Display	PDB format
PDBx/mmJSON format	3qvo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3qvo_validation.pdf.gz	447 KB	Display	wwPDB validaton report
Full document	3qvo_full_validation.pdf.gz	448.7 KB	Display
Data in XML	3qvo_validation.xml.gz	11.7 KB	Display
Data in CIF	3qvo_validation.cif.gz	15 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qv/3qvo ftp://data.pdbj.org/pub/pdb/validation_reports/qv/3qvo	HTTPS FTP

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Related structure data

Similar structure data	1agj-1 5xj9-d 3n36-d 6y43-d 1rc2-2 6d60-d 4ef5-d 1dua-d 2yz4-d 1due-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc27541

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NmrA family protein

hetero molecules

26.6 kDa, 1 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)	73.524, 73.524, 130.246
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	91
Space group name H-M	P4₁22

Details

THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

#1: Protein	NmrA family protein / Rossman-fold NAD(P)-binding protein Mass: 26416.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 2457T / Gene: S1416, SF2457T_2192 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E3Y2F5
#2: Chemical	ChemComp-MNB / 5-MERCAPTO-2-NITRO-BENZOIC ACID Mass: 199.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₅NO₄S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.34 Å³/Da / Density % sol: 63.14 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 1M potassium/sodium phosphate pH 6.9, 1.25mM DNTB, 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97953, 0.97940

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 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	0.97953	1
2	0.9794	1

Reflection

Redundancy: 15.2 % / Av σ(I) over netI: 34.06 / Number: 236700 / R_merge(I) obs: 0.114 / Χ²: 1.32 / D res high: 2.35 Å / D res low: 50 Å / Num. obs: 15548 / % possible obs: 99.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.37	50	95	1	0.093	3.486	12.7
5.06	6.37	99.9	1	0.096	2.857	14.4
4.42	5.06	99.9	1	0.096	2.489	14.8
4.02	4.42	100	1	0.102	2.274	15.1
3.73	4.02	99.9	1	0.097	1.88	15.3
3.51	3.73	100	1	0.107	1.698	15.5
3.33	3.51	100	1	0.112	1.461	15.6
3.19	3.33	100	1	0.128	1.21	15.7
3.07	3.19	100	1	0.141	1.109	15.8
2.96	3.07	100	1	0.155	0.986	15.7
2.87	2.96	100	1	0.198	0.877	15.8
2.79	2.87	100	1	0.246	0.805	15.9
2.71	2.79	100	1	0.288	0.759	15.9
2.65	2.71	100	1	0.304	0.771	15.9
2.59	2.65	100	1	0.39	0.712	15.8
2.53	2.59	100	1	0.45	0.66	16
2.48	2.53	100	1	0.533	0.665	15.6
2.43	2.48	100	1	0.587	0.636	15.2
2.39	2.43	100	1	0.581	0.621	14.6
2.35	2.39	100	1	0.654	0.628	13.5

Reflection

Resolution: 2.3→50 Å / Num. all: 16455 / Num. obs: 16455 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / R_merge(I) obs: 0.082 / Net I/σ(I): 8.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.3-2.34	10.7	0.645	1	100
2.34-2.38	11.2	0.537	1	100
2.38-2.43	11.8	0.456	1	100
2.43-2.48	11.9	0.428	1	100
2.48-2.53	11.9	0.368	1	100
2.53-2.59	12.1	0.325	1	100
2.59-2.66	12	0.269	1	100
2.66-2.73	11.9	0.216	1	100
2.73-2.81	12	0.208	1	100
2.81-2.9	11.9	0.168	1	100
2.9-3	11.9	0.131	1	100
3-3.12	11.8	0.111	1	100
3.12-3.26	11.8	0.099	1	100
3.26-3.44	11.9	0.084	1	100
3.44-3.65	11.7	0.078	1	100
3.65-3.93	11.6	0.071	1	99.9
3.93-4.33	11.5	0.076	1	99.6
4.33-4.95	11.2	0.075	1	99.6
4.95-6.24	10.9	0.065	1	99.7
6.24-50	9.7	0.061	1	91.5

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.35 Å / D res low: 50 Å / FOM : 0.295 / FOM acentric: 0.329 / FOM centric: 0.131 / Reflection: 15423 / Reflection acentric: 12800 / Reflection centric: 2623

Phasing MAD set

Highest resolution: 2.35 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	1.29	1	0.1	0.1	0	0	12800	2623
2	0.99	0.96	6	10.2	0.26	0.21	12781	2599

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	14.15-50	1.3	1	1	0.6	0	0	32	51
1	8.24-14.15	1	1	0.9	0.6	0	0	183	118
1	5.81-8.24	1.12	1	0.5	0.4	0	0	499	216
1	4.49-5.81	1.3	1	0.4	0.3	0	0	951	296
1	3.66-4.49	1.11	1	0.2	0.2	0	0	1538	368
1	3.09-3.66	1.43	1	0.1	0.1	0	0	2280	448
1	2.67-3.09	4.43	1	0	0	0	0	3153	524
1	2.35-2.67	1.6	1	0	0	0	0	4164	602
2	14.15-50	0.99	0.94	23.4	26.8	0.5	0.35	27	44
2	8.24-14.15	0.98	0.96	25.7	23.5	0.33	0.3	170	111
2	5.81-8.24	0.96	0.93	13.4	17.2	0.47	0.32	499	213
2	4.49-5.81	0.97	0.95	11.9	15.8	0.36	0.25	951	292
2	3.66-4.49	0.99	0.97	9.4	14	0.28	0.18	1537	365
2	3.09-3.66	0.99	0.97	5.7	8.3	0.25	0.18	2280	448
2	2.67-3.09	0.99	0.98	3.8	5.4	0.18	0.14	3153	524
2	2.35-2.67	1	1	3.4	4.9	0.1	0.07	4164	602

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	111.7398	0.86	0.975	0.057	7.172	0
2	99.3223	0.901	0.937	0.184	4.93	0
3	96.0561	0.856	0.894	0.204	3.97	0
4	157.1207	0.838	0.548	0.203	4.946	0
5	92.771	1.145	0.879	0.154	4.016	0
6	101.108	0.86	0.974	0.058	3.913	-0.082
7	94.4571	0.901	0.937	0.184	2.815	-0.072
8	94.1694	0.856	0.893	0.204	2.45	-0.027
9	164.3808	0.838	0.548	0.203	2.916	-0.056
10	82.7929	1.145	0.879	0.154	2.173	-0.042

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
14.15-50	0.344	0.604	0.181	83	32	51
8.24-14.15	0.399	0.563	0.145	301	183	118
5.81-8.24	0.534	0.664	0.234	715	499	216
4.49-5.81	0.511	0.604	0.215	1247	951	296
3.66-4.49	0.478	0.55	0.177	1906	1538	368
3.09-3.66	0.41	0.459	0.16	2728	2280	448
2.67-3.09	0.242	0.267	0.094	3677	3153	524
2.35-2.67	0.098	0.108	0.029	4766	4164	602

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 15423

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.54-100	62.5	0.618	506
5.99-7.54	54.7	0.873	505
5.2-5.99	53.4	0.887	510
4.72-5.2	51.4	0.91	513
4.37-4.72	55.9	0.911	501
4.1-4.37	56.2	0.907	507
3.89-4.1	56.7	0.895	503
3.72-3.89	60.4	0.881	505
3.57-3.72	61.1	0.876	511
3.44-3.57	57.4	0.88	536
3.32-3.44	60.2	0.86	545
3.21-3.32	60.8	0.848	564
3.11-3.21	62.1	0.868	583
3.02-3.11	62.9	0.832	602
2.94-3.02	61.6	0.837	604
2.87-2.94	65.7	0.83	630
2.8-2.87	68.6	0.835	655
2.73-2.8	69.4	0.803	648
2.67-2.73	71	0.843	689
2.61-2.67	69.5	0.84	667
2.56-2.61	74.9	0.799	714
2.51-2.56	75	0.83	722
2.46-2.51	79.9	0.797	715
2.42-2.46	77.4	0.822	737
2.35-2.42	80.4	0.694	1251

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Processing

Software

Name	Version	Classification
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: 2.3→36.76 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.962 / SU ML: 0.135 / SU R Cruickshank DPI: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.189
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25075	831	5.1 %	RANDOM
R_work	0.21481	-	-	-
obs	0.21652	15584	99.44 %	-
all	-	15584	-	-

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 mean: 56.042 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.63 Å²	0 Å²	0 Å²
2-	-	2.63 Å²	0 Å²
3-	-	-	-5.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→36.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1508	0	13	75	1596

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	1560
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1043
X-RAY DIFFRACTION	r_angle_refined_deg	1.621	1.978	2116
X-RAY DIFFRACTION	r_angle_other_deg	0.884	3.001	2564
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.182	5	197
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.747	25.455	66
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.586	15	274
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.397	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	243
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	1728
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	278
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.814	1.5	983
X-RAY DIFFRACTION	r_mcbond_other	0.189	1.5	398
X-RAY DIFFRACTION	r_mcangle_it	1.544	2	1585
X-RAY DIFFRACTION	r_scbond_it	2.702	3	577
X-RAY DIFFRACTION	r_scangle_it	4.469	4.5	530
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.302→2.361 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	62	-
R_work	0.268	1111	-
obs	-	-	99.41 %

Refinement TLS params.

Method: refined / Origin x: 17.9993 Å / Origin y: 9.2326 Å / Origin z: 10.4409 Å

	11	12	13	21	22	23	31	32	33
T	0.0593 Å²	0.0176 Å²	0.0348 Å²	-	0.3849 Å²	-0.0852 Å²	-	-	0.1397 Å²
L	4.3302 °²	1.773 °²	-0.1687 °²	-	1.9956 °²	-0.7443 °²	-	-	3.4218 °²
S	0.22 Å °	-0.1399 Å °	0.1682 Å °	0.1196 Å °	-0.1269 Å °	-0.167 Å °	0.2046 Å °	0.7473 Å °	-0.0931 Å °

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