PDB-4qne: Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, dele...

Basic information

• Entry: Database: PDB / ID: 4qne
• Title: Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with NAD and IMP
• Components: Inosine 5'-monophosphate dehydrogenase
• Keywords: OXIDOREDUCTASE / structural genomics / IMPDH / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / IMP / NAD acidic form

Function / homology

Function:

IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm

Domain/homology:

IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta

Component:

INOSINIC ACID / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Inosine-5'-monophosphate dehydrogenase

• Biological species: Vibrio cholerae O1 biovar El Tor (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
• Authors: Osipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
• Citation: Journal: To be Published; Title: Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with NAD and IMP; Authors: Osipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Jun 17, 2014	Deposition site: RCSB / Processing site: RCSB
Supersession	Aug 6, 2014	ID: 4HLV
Revision 1.0	Aug 6, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 26, 2017	Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Inosine 5'-monophosphate dehydrogenase

B: Inosine 5'-monophosphate dehydrogenase

hetero molecules

Summary:

• 78.6 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	78,597	8
Polymers	76,495	2
Non-polymers	2,101	6
Water	3,207	178

1

A: Inosine 5'-monophosphate dehydrogenase

B: Inosine 5'-monophosphate dehydrogenase

hetero molecules

A: Inosine 5'-monophosphate dehydrogenase

B: Inosine 5'-monophosphate dehydrogenase

hetero molecules

A: Inosine 5'-monophosphate dehydrogenase

B: Inosine 5'-monophosphate dehydrogenase

hetero molecules

A: Inosine 5'-monophosphate dehydrogenase

B: Inosine 5'-monophosphate dehydrogenase

hetero molecules

Summary:

• defined by author&software
• 314 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	314,387	32
Polymers	305,982	8
Non-polymers	8,406	24
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-x+1,-y,z	1
crystal symmetry operation	3_545	-y+1/2,x-1/2,z	1
crystal symmetry operation	4_555	y+1/2,-x+1/2,z	1

Calculated values:

Buried area	57380 Å2
ΔGint	-276 kcal/mol
Surface area	82140 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	121.334, 121.334, 94.470
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P4212

Components

#1: Protein

A B Inosine 5'-monophosphate dehydrogenase

Details:

Mass: 38247.703 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC0767 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KTW3, IMP dehydrogenase

#2: Chemical

A-501 B-501 ChemComp-IMP / INOSINIC ACID / Inosinic acid

Details:

Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₄O₈P

#3: Chemical

A-502 B-502 ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Nicotinamide adenine dinucleotide

Details:

Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂

#4: Chemical

A-503 B-503 ChemComp-K / POTASSIUM ION

Details:

Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

#5: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H₂O

• Sequence details: RESIDUES 91-219 ARE DELETED AND REPLACED WITH AN SGG LINKER.

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.27 ų/Da / Density % sol: 45.88 %
• Crystal grow: Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 ; Details: 0.77 M sodium/potassium phosphate, 0.15 M Tris, 6% MPD, 0.02 M NAD, 0.02 M XMP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
• Detector: Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 20, 2012
• Radiation: Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9792 Å / Relative weight: 1
• Reflection: Resolution: 2.319→94.47 Å / Num. all: 31196 / Num. obs: 31196 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / R_merge(I) obs: 0.104 / Net I/σ(I): 8.8

Reflection shell

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.319-2.36	6.6	0.918	2.1	1	100
2.36-2.4	6.8	0.821		1	100
2.4-2.45	7.2	0.732		1	100
2.45-2.5	7.6	0.609		1	100
2.5-2.55	8.1	0.538		1	100
2.55-2.61	8.9	0.526		1	100
2.61-2.68	9.1	0.416		1	100
2.68-2.75	9.1	0.414		1	100
2.75-2.83	9.1	0.298		1	100
2.83-2.92	9.2	0.256		1	100
2.92-3.03	9.2	0.213		1	99.9
3.03-3.15	9.2	0.174		1	100
3.15-3.29	9.3	0.133		1	100
3.29-3.47	9.4	0.101		1	100
3.47-3.68	9.5	0.084		1	100
3.68-3.97	9.5	0.069		1	100
3.97-4.37	9.5	0.061		1	100
4.37-5	9.4	0.056		1	99.9
5-6.29	9.3	0.057		1	100
6.29-50	8.5	0.056		1	99.5

Processing

Software

Name	Version	Classification	NB
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.8.0071	refinement
PDB_EXTRACT	3.14	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing
HKL-3000		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FO4

4fo4

Resolution: 2.32→47.5 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.931 / SU B: 17.244 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.27019	1553	5 %	RANDOM
Rwork	0.1963	-	-	-
obs	0.2	29325	99.04 %	-
all	-	30878	-	-

• 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 mean: 43.852 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-1.48 Å2	-0 Å2	0 Å2
2-	-	-1.48 Å2	-0 Å2
3-	-	-	2.95 Å2

Refinement step

Cycle: LAST / Resolution: 2.32→47.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4984	0	136	178	5298

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	5325
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	5200
X-RAY DIFFRACTION	r_angle_refined_deg	1.852	2.002	7251
X-RAY DIFFRACTION	r_angle_other_deg	0.874	3	11957
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.627	5	710
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.781	23.769	199
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.361	15	887
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.841	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	851
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6037
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1146
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	2.609	3.199	2764
X-RAY DIFFRACTION	r_mcbond_other	2.601	3.198	2763
X-RAY DIFFRACTION	r_mcangle_it	3.776	4.786	3456
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.169	3.651	2561
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.319→2.379 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.314	94	-
Rwork	0.256	2152	-
obs	-	-	99.69 %

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	0.5222	0.07	-0.0615	0.1944	-0.1916	0.2206	0.0022	-0.0173	0.0186	0.0573	-0.0325	-0.0624	-0.0254	0.0537	0.0303	0.0808	-0.0251	-0.0519	0.1232	-0.0263	0.0589	85.9114	11.4565	14.4806
2	0.2757	-0.0847	0.0083	0.4839	-0.0823	0.51	0.0699	0.0667	0.0297	-0.0309	0.0081	0.0022	-0.1823	0.1049	-0.0781	0.21	-0.0564	0.0644	0.0814	-0.0004	0.0298	71.3585	25.6033	-32.2321

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 503
2	X-RAY DIFFRACTION	2	B	5 - 503