PDB-4ns3: Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogen...

ID or keywords:

Entry

Database: PDB / ID: 4ns3

Title

Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD and cobalamin

Components

Delta-1-pyrroline-5-carboxylate dehydrogenase

Keywords

OXIDOREDUCTASE / Rossmann Fold / dehydrogenase / dehydrogenation

Function / homology

Function and homology information

L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / cytoplasmic side of plasma membrane / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.38 Å

Authors

Lagautriere, T. / Bashiri, G. / Baker, E.N.

Citation

Journal: J.Struct.Biol. / Year: 2015
Title: Use of a "silver bullet" to resolve crystal lattice dislocation disorder: A cobalamin complex of Delta (1)-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis.
Authors: Lagautriere, T. / Bashiri, G. / Baker, E.N.

History

Deposition	Nov 27, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 4, 2015	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Jul 17, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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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PDBx/mmCIF format	4ns3.cif.gz	679.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4ns3.ent.gz	554.9 KB	Display	PDB format
PDBx/mmJSON format	4ns3.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ns3_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	4ns3_full_validation.pdf.gz	2.9 MB	Display
Data in XML	4ns3_validation.xml.gz	160.2 KB	Display
Data in CIF	4ns3_validation.cif.gz	218.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ns/4ns3 ftp://data.pdbj.org/pub/pdb/validation_reports/ns/4ns3	HTTPS FTP

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Related structure data

Related structure data	4lemC C: citing same article (ref.)
Similar structure data	4jdc-2 4lem-d 4ihi-2 4idm-2 2ehq-2 2ej6-2 2iy6-1 2bhq-1 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
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: Delta-1-pyrroline-5-carboxylate dehydrogenase

B: Delta-1-pyrroline-5-carboxylate dehydrogenase

C: Delta-1-pyrroline-5-carboxylate dehydrogenase

D: Delta-1-pyrroline-5-carboxylate dehydrogenase

E: Delta-1-pyrroline-5-carboxylate dehydrogenase

F: Delta-1-pyrroline-5-carboxylate dehydrogenase

hetero molecules

374 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	164.855, 164.855, 260.242
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	MET	MET	A	A	0 - 540	20 - 560
2	1	HIS	HIS	MET	MET	B	B	0 - 540	20 - 560
1	2	HIS	HIS	MET	MET	A	A	0 - 540	20 - 560
2	2	HIS	HIS	MET	MET	C	C	0 - 540	20 - 560
1	3	HIS	HIS	MET	MET	A	A	0 - 540	20 - 560
2	3	HIS	HIS	MET	MET	D	D	0 - 540	20 - 560
1	4	HIS	HIS	ALA	ALA	A	A	0 - 541	20 - 561
2	4	HIS	HIS	ALA	ALA	E	E	0 - 541	20 - 561
1	5	MET	MET	ALA	ALA	A	A	1 - 541	21 - 561
2	5	MET	MET	ALA	ALA	F	F	1 - 541	21 - 561
1	6	HIS	HIS	ALA	ALA	B	B	0 - 541	20 - 561
2	6	HIS	HIS	ALA	ALA	C	C	0 - 541	20 - 561
1	7	HIS	HIS	ALA	ALA	B	B	0 - 541	20 - 561
2	7	HIS	HIS	ALA	ALA	D	D	0 - 541	20 - 561
1	8	HIS	HIS	VAL	VAL	B	B	0 - 542	20 - 562
2	8	HIS	HIS	VAL	VAL	E	E	0 - 542	20 - 562
1	9	MET	MET	ALA	ALA	B	B	1 - 541	21 - 561
2	9	MET	MET	ALA	ALA	F	F	1 - 541	21 - 561
1	10	HIS	HIS	ASP	ASP	C	C	0 - 543	20 - 563
2	10	HIS	HIS	ASP	ASP	D	D	0 - 543	20 - 563
1	11	HIS	HIS	VAL	VAL	C	C	0 - 542	20 - 562
2	11	HIS	HIS	VAL	VAL	E	E	0 - 542	20 - 562
1	12	MET	MET	ALA	ALA	C	C	1 - 541	21 - 561
2	12	MET	MET	ALA	ALA	F	F	1 - 541	21 - 561
1	13	HIS	HIS	VAL	VAL	D	D	0 - 542	20 - 562
2	13	HIS	HIS	VAL	VAL	E	E	0 - 542	20 - 562
1	14	MET	MET	ALA	ALA	D	D	1 - 541	21 - 561
2	14	MET	MET	ALA	ALA	F	F	1 - 541	21 - 561
1	15	MET	MET	ALA	ALA	E	E	1 - 541	21 - 561
2	15	MET	MET	ALA	ALA	F	F	1 - 541	21 - 561

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.45806, 0.316925, -0.830506), (0.313509, -0.816653, -0.484552), (-0.831801, -0.482325, 0.274717)	-63.78868, 11.1266, -37.41512
3	given	(-0.938306, -0.316321, 0.139723), (-0.315523, 0.617787, -0.720267), (0.141517, -0.719917, -0.679479)	-122.70072, -5.61304, 41.45669
4	given	(0.216491, 0.934548, 0.282404), (-0.109316, -0.26424, 0.958242), (0.970145, -0.238322, 0.044956)	-43.81471, -43.20963, 78.49236

#1: Protein	Delta-1-pyrroline-5-carboxylate dehydrogenase / Pyrroline-5-carboxylate dehydrogenase RocA Mass: 61210.691 Da / Num. of mol.: 6 / Mutation: G505D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1224, pruA, rocA, Rv1187 / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): Mc2 4517 References: UniProt: L7N4Z6, UniProt: O50443*PLUS, EC: 1.5.1.12
#2: Chemical	ChemComp-B12 / COBALAMIN Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆₂H₈₉CoN₁₃O₁₄P
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2631 / 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: 2.78 Å³/Da / Density % sol: 55.75 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 0.1 M Bicine/Tris pH 8.1, 12% PEG 1000, 12% PEG 3350, 12% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulphate, 0.2% w/v biotin, 0.2% w/v phospho(enol) ...Details: 0.1 M Bicine/Tris pH 8.1, 12% PEG 1000, 12% PEG 3350, 12% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulphate, 0.2% w/v biotin, 0.2% w/v phospho(enol)pyruvic acid monosodium salt hydrate, 0.2% w/v D-(+)-Melezitose hydrate, 0.2% w/v cobalamin and 0.02M HEPES sodium pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal

Density Matthews: 2.78 Å³/Da / Density % sol: 55.75 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.1 M Bicine/Tris pH 8.1, 12% PEG 1000, 12% PEG 3350, 12% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulphate, 0.2% w/v biotin, 0.2% w/v phospho(enol) ...

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953691 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953691 Å / Relative weight: 1
Reflection	Resolution: 2.38→20.05 Å / Num. obs: 164364 / % possible obs: 99.4 %

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
MOLREP		phasing
REFMAC	5.8.0049	refinement
XDS		data reduction
SCALA		data scaling
Blu-Ice	Ice	data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.38→20.049 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.948 / SU ML: 0.17 / σ(F): 1.34 / Phase error: 19.73 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.2051	8211	5.02 %
R_work	0.1566	-	-
obs	0.1591	163475	99.72 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.398 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.25 Å²	-0.12 Å²	0 Å²
2-	-	-0.25 Å²	0 Å²
3-	-	-	0.81 Å²

Refinement step

Cycle: LAST / Resolution: 2.38→20.049 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24843	0	418	2631	27892

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	25914
X-RAY DIFFRACTION	f_angle_d	1.343	35456
X-RAY DIFFRACTION	f_dihedral_angle_d	14.604	9250
X-RAY DIFFRACTION	f_chiral_restr	0.115	3933
X-RAY DIFFRACTION	f_plane_restr	0.006	4637

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	33034	0.04
1	2	B	33034	0.04
2	1	A	32786	0.05
2	2	C	32786	0.05
3	1	A	32771	0.05
3	2	D	32771	0.05
4	1	A	32456	0.05
4	2	E	32456	0.05
5	1	A	32345	0.06
5	2	F	32345	0.06
6	1	B	32742	0.05
6	2	C	32742	0.05
7	1	B	32744	0.05
7	2	D	32744	0.05
8	1	B	32482	0.06
8	2	E	32482	0.06
9	1	B	32366	0.06
9	2	F	32366	0.06
10	1	C	32723	0.06
10	2	D	32723	0.06
11	1	C	32514	0.06
11	2	E	32514	0.06
12	1	C	32505	0.06
12	2	F	32505	0.06
13	1	D	32560	0.05
13	2	E	32560	0.05
14	1	D	32457	0.06
14	2	F	32457	0.06
15	1	E	32383	0.05
15	2	F	32383	0.05

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 (%)
2.38-2.4043	0.3593	260	0.2798	4708	X-RAY DIFFRACTION	92
2.4043-2.4326	0.2632	269	0.2206	5147	X-RAY DIFFRACTION	100
2.4326-2.4622	0.2663	301	0.2166	5130	X-RAY DIFFRACTION	100
2.4622-2.4933	0.2696	269	0.2068	5125	X-RAY DIFFRACTION	100
2.4933-2.526	0.2746	268	0.2021	5182	X-RAY DIFFRACTION	100
2.526-2.5606	0.2448	243	0.1967	5131	X-RAY DIFFRACTION	100
2.5606-2.5971	0.2582	264	0.1844	5134	X-RAY DIFFRACTION	100
2.5971-2.6358	0.2527	284	0.184	5146	X-RAY DIFFRACTION	100
2.6358-2.6769	0.2385	300	0.1837	5150	X-RAY DIFFRACTION	100
2.6769-2.7206	0.2508	281	0.1865	5122	X-RAY DIFFRACTION	100
2.7206-2.7674	0.2502	276	0.1852	5131	X-RAY DIFFRACTION	100
2.7674-2.8176	0.245	285	0.1739	5155	X-RAY DIFFRACTION	100
2.8176-2.8717	0.2346	249	0.1676	5206	X-RAY DIFFRACTION	100
2.8717-2.9301	0.2554	248	0.184	5170	X-RAY DIFFRACTION	100
2.9301-2.9936	0.2395	227	0.1704	5244	X-RAY DIFFRACTION	100
2.9936-3.063	0.2328	257	0.1671	5168	X-RAY DIFFRACTION	100
3.063-3.1393	0.2112	270	0.1673	5196	X-RAY DIFFRACTION	100
3.1393-3.2239	0.2248	270	0.1617	5139	X-RAY DIFFRACTION	100
3.2239-3.3183	0.2163	257	0.1576	5191	X-RAY DIFFRACTION	100
3.3183-3.4249	0.2019	309	0.1557	5175	X-RAY DIFFRACTION	100
3.4249-3.5467	0.2004	298	0.1509	5162	X-RAY DIFFRACTION	100
3.5467-3.6879	0.1861	294	0.1457	5168	X-RAY DIFFRACTION	100
3.6879-3.8546	0.1786	285	0.1429	5224	X-RAY DIFFRACTION	100
3.8546-4.0562	0.1856	267	0.1328	5186	X-RAY DIFFRACTION	100
4.0562-4.308	0.1712	255	0.1277	5230	X-RAY DIFFRACTION	100
4.308-4.6368	0.1542	300	0.1144	5213	X-RAY DIFFRACTION	100
4.6368-5.0965	0.1483	280	0.1167	5250	X-RAY DIFFRACTION	100
5.0965-5.8182	0.1619	275	0.1354	5295	X-RAY DIFFRACTION	100
5.8182-7.2717	0.1882	294	0.1445	5308	X-RAY DIFFRACTION	100
7.2717-20.0497	0.1492	276	0.1368	5478	X-RAY DIFFRACTION	100

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