PDB-2rc5: Refined structure of FNR from Leptospira interrogans

ID or keywords:

Entry

Database: PDB / ID: 2rc5

Title

Refined structure of FNR from Leptospira interrogans

Components

Ferredoxin-NADP reductase

Keywords

OXIDOREDUCTASE / FAD

Function / homology

Function and homology information

oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Leptospira interrogans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.431 Å

Authors

Nascimento, A.S. / Catalano-Dupuy, D.L. / Polikarpov, I. / Ceccarelli, E.A.

Citation

Journal: Bmc Struct.Biol. / Year: 2007
Title: Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+.
Authors: Nascimento, A.S. / Catalano-Dupuy, D.L. / Bernardes, A. / Neto, M.O. / Santos, M.A. / Ceccarelli, E.A. / Polikarpov, I.

History

Deposition	Sep 19, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 25, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_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	2rc5.cif.gz	517 KB	Display	PDBx/mmCIF format
PDB format	pdb2rc5.ent.gz	426.6 KB	Display	PDB format
PDBx/mmJSON format	2rc5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2rc5_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	2rc5_full_validation.pdf.gz	1.5 MB	Display
Data in XML	2rc5_validation.xml.gz	69.8 KB	Display
Data in CIF	2rc5_validation.cif.gz	98.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rc/2rc5 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/2rc5	HTTPS FTP

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Related structure data

Related structure data	2rc6C C: citing same article (ref.)
Similar structure data	1vsl-1 2rc6-2 5ts9-2 4uyz-4 2rc6-3 1vsk-1 6yun-d 1vsm-1 6ru8-4 2ghi-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

2rc6C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#133 - Jan 2011 Nitric Oxide Synthase similarity (3) #228 - Dec 2018 Directed Evolution of Enzymes similarity (3)

Deposited unit

A: Ferredoxin-NADP reductase

B: Ferredoxin-NADP reductase

C: Ferredoxin-NADP reductase

D: Ferredoxin-NADP reductase

hetero molecules

144 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ferredoxin-NADP reductase

hetero molecules

defined by author&software
36 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ferredoxin-NADP reductase

hetero molecules

defined by author&software
35.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Ferredoxin-NADP reductase

hetero molecules

defined by author&software
36 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Ferredoxin-NADP reductase

hetero molecules

defined by author&software
35.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.112, 111.832, 89.913
Angle α, β, γ (deg.)	90.00, 92.76, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ferredoxin-NADP reductase Mass: 34967.098 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans (bacteria) / Plasmid: pEt32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EY89, ferredoxin-NADP+ reductase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1238 / 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: 2.34 Å³/Da / Density % sol: 47.38 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 7 Details: 27% PEG3350, 0.3M ammonium fluoride, 50mM Tris-HCL buffer, pH 7.0, vapor diffusion, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

LNLS

/ Beamline: D03B-MX1 / Wavelength: 1.42 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2005 / Details: mirrors

Radiation

Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.42 Å / Relative weight: 1

Reflection

Resolution: 2.43→89.809 Å / Num. all: 48995 / Num. obs: 47770 / % possible obs: 97.5 % / Redundancy: 2.8 % / R_merge(I) obs: 0.049 / R_sym value: 0.049 / Net I/σ(I): 5.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.42-2.55	2.6	0.144	2.3	16067	6299	0.144	88.5
2.55-2.71	2.8	0.108	4.3	18892	6778	0.108	99.9
2.71-2.89	2.8	0.08	6	17559	6281	0.08	99.7
2.89-3.13	2.8	0.062	10.8	16644	5907	0.062	99.6
3.13-3.42	2.8	0.052	2.7	15310	5400	0.052	99.4
3.42-3.83	2.9	0.039	16.1	13920	4874	0.039	99.2
3.83-4.42	2.9	0.034	17.4	12269	4285	0.034	98.8
4.42-5.41	2.9	0.035	17	10539	3643	0.035	98.2
5.41-7.66	2.9	0.042	14.2	8062	2766	0.042	97.5
7.66-56.25	2.9	0.033	14	4419	1537	0.033	95.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.431→44.904 Å / FOM work R set: 0.813

	R_factor	Num. reflection	% reflection
R_free	0.255	2413	5.06 %
R_work	0.225	-	-
obs	-	47690	98.47 %

Solvent computation

B_sol: 16.443 Å² / k_sol: 0.358 e/Å³

Displacement parameters

B_iso max: 63.23 Å² / B_iso mean: 26.43 Å² / B_iso min: 20.44 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.702 Å²	-0 Å²	-1.269 Å²
2-	-	0.248 Å²	-0 Å²
3-	-	-	-2.95 Å²

Refinement step

Cycle: LAST / Resolution: 2.431→44.904 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9477	0	248	1238	10963

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.431-2.44	0.289	283	X-RAY DIFFRACTION	91	56
2.44-2.449	0.284	474	X-RAY DIFFRACTION	91	89
2.449-2.458	0.283	501	X-RAY DIFFRACTION	91	94
2.458-2.467	0.277	496	X-RAY DIFFRACTION	91	95
2.467-2.477	0.291	510	X-RAY DIFFRACTION	91	95
2.477-2.487	0.268	511	X-RAY DIFFRACTION	91	93
2.487-2.497	0.268	493	X-RAY DIFFRACTION	91	94
2.497-2.507	0.247	482	X-RAY DIFFRACTION	91	95
2.507-2.517	0.262	529	X-RAY DIFFRACTION	91	94
2.517-2.527	0.259	470	X-RAY DIFFRACTION	91	95
2.527-2.537	0.271	506	X-RAY DIFFRACTION	91	95
2.537-2.548	0.257	494	X-RAY DIFFRACTION	91	96
2.548-2.559	0.272	502	X-RAY DIFFRACTION	91	94
2.559-2.57	0.261	506	X-RAY DIFFRACTION	91	95
2.57-2.581	0.264	524	X-RAY DIFFRACTION	91	96
2.581-2.593	0.252	493	X-RAY DIFFRACTION	91	94
2.593-2.604	0.281	514	X-RAY DIFFRACTION	91	94
2.604-2.616	0.269	502	X-RAY DIFFRACTION	91	96
2.616-2.628	0.266	480	X-RAY DIFFRACTION	91	94
2.628-2.64	0.278	521	X-RAY DIFFRACTION	91	95
2.64-2.653	0.248	518	X-RAY DIFFRACTION	91	96
2.653-2.666	0.266	480	X-RAY DIFFRACTION	91	95
2.666-2.679	0.276	499	X-RAY DIFFRACTION	91	96
2.679-2.692	0.244	526	X-RAY DIFFRACTION	91	93
2.692-2.705	0.257	526	X-RAY DIFFRACTION	91	96
2.705-2.719	0.254	492	X-RAY DIFFRACTION	91	95
2.719-2.733	0.248	486	X-RAY DIFFRACTION	91	95
2.733-2.748	0.267	512	X-RAY DIFFRACTION	91	96
2.748-2.762	0.279	479	X-RAY DIFFRACTION	91	94
2.762-2.777	0.26	506	X-RAY DIFFRACTION	91	94
2.777-2.793	0.254	500	X-RAY DIFFRACTION	91	95
2.793-2.809	0.256	538	X-RAY DIFFRACTION	91	95
2.809-2.825	0.262	483	X-RAY DIFFRACTION	91	94
2.825-2.841	0.235	494	X-RAY DIFFRACTION	91	94
2.841-2.858	0.256	501	X-RAY DIFFRACTION	91	95
2.858-2.875	0.241	514	X-RAY DIFFRACTION	91	95
2.875-2.893	0.235	499	X-RAY DIFFRACTION	91	95
2.893-2.911	0.228	509	X-RAY DIFFRACTION	91	96
2.911-2.929	0.233	491	X-RAY DIFFRACTION	91	94
2.929-2.948	0.259	529	X-RAY DIFFRACTION	91	96
2.948-2.968	0.233	472	X-RAY DIFFRACTION	91	96
2.968-2.988	0.248	522	X-RAY DIFFRACTION	91	92
2.988-3.008	0.234	484	X-RAY DIFFRACTION	91	92
3.008-3.03	0.253	493	X-RAY DIFFRACTION	91	94
3.03-3.051	0.232	505	X-RAY DIFFRACTION	91	94
3.051-3.074	0.219	518	X-RAY DIFFRACTION	91	96
3.074-3.097	0.246	506	X-RAY DIFFRACTION	91	95
3.097-3.121	0.215	506	X-RAY DIFFRACTION	91	94
3.121-3.145	0.233	468	X-RAY DIFFRACTION	91	95
3.145-3.171	0.22	520	X-RAY DIFFRACTION	91	94
3.171-3.197	0.232	503	X-RAY DIFFRACTION	91	96
3.197-3.224	0.223	503	X-RAY DIFFRACTION	91	93
3.224-3.252	0.231	512	X-RAY DIFFRACTION	91	96
3.252-3.281	0.201	484	X-RAY DIFFRACTION	91	93
3.281-3.311	0.202	511	X-RAY DIFFRACTION	91	95
3.311-3.342	0.2	504	X-RAY DIFFRACTION	91	96
3.342-3.375	0.207	504	X-RAY DIFFRACTION	91	95
3.375-3.408	0.206	520	X-RAY DIFFRACTION	91	94
3.408-3.444	0.205	490	X-RAY DIFFRACTION	91	93
3.444-3.48	0.199	495	X-RAY DIFFRACTION	91	94
3.48-3.518	0.173	489	X-RAY DIFFRACTION	91	94
3.518-3.558	0.202	495	X-RAY DIFFRACTION	91	94
3.558-3.6	0.193	520	X-RAY DIFFRACTION	91	94
3.6-3.644	0.177	479	X-RAY DIFFRACTION	91	93
3.644-3.69	0.192	505	X-RAY DIFFRACTION	91	94
3.69-3.739	0.185	494	X-RAY DIFFRACTION	91	93
3.739-3.79	0.189	499	X-RAY DIFFRACTION	91	93
3.79-3.844	0.189	500	X-RAY DIFFRACTION	91	94
3.844-3.901	0.195	503	X-RAY DIFFRACTION	91	93
3.901-3.962	0.179	481	X-RAY DIFFRACTION	91	92
3.962-4.027	0.185	499	X-RAY DIFFRACTION	91	94
4.027-4.097	0.184	501	X-RAY DIFFRACTION	91	93
4.097-4.171	0.171	500	X-RAY DIFFRACTION	91	94
4.171-4.251	0.182	484	X-RAY DIFFRACTION	91	94
4.251-4.338	0.166	531	X-RAY DIFFRACTION	91	94
4.338-4.432	0.189	488	X-RAY DIFFRACTION	91	95
4.432-4.535	0.175	496	X-RAY DIFFRACTION	91	93
4.535-4.648	0.176	517	X-RAY DIFFRACTION	91	94
4.648-4.774	0.176	481	X-RAY DIFFRACTION	91	91
4.774-4.914	0.185	490	X-RAY DIFFRACTION	91	92
4.914-5.073	0.209	495	X-RAY DIFFRACTION	91	94
5.073-5.254	0.196	492	X-RAY DIFFRACTION	91	93
5.254-5.464	0.221	513	X-RAY DIFFRACTION	91	94
5.464-5.712	0.221	504	X-RAY DIFFRACTION	91	92
5.712-6.012	0.227	499	X-RAY DIFFRACTION	91	93
6.012-6.388	0.229	496	X-RAY DIFFRACTION	91	92
6.388-6.88	0.227	494	X-RAY DIFFRACTION	91	93
6.88-7.569	0.22	500	X-RAY DIFFRACTION	91	92
7.569-8.658	0.203	483	X-RAY DIFFRACTION	91	90
8.658-10.882	0.189	505	X-RAY DIFFRACTION	91	91
10.882-44.912	0.271	451	X-RAY DIFFRACTION	91	81

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