PDB-4x3z: Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, dele...

Basic information

• Entry: Database: PDB / ID: 4x3z
• Title: Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with XMP and NAD
• Components: Inosine-5'-monophosphate dehydrogenase
• Keywords: OXIDOREDUCTASE / INOSINE 5'-MONOPHOSPHATE DEHYDROGENASE / IMPDH / XMP / xanthosine monophosphate / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID

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:

: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / XANTHOSINE-5'-MONOPHOSPHATE / Inosine-5'-monophosphate dehydrogenase

• Biological species: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
• Authors: Osipiuk, J. / MALTSEVA, N. / KIM, Y. / Mulligan, R. / 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 XMP and NAD; Authors: Osipiuk, J. / MALTSEVA, N. / KIM, Y. / Mulligan, R. / MAKOWSKA-GRZYSKA, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 2, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Derived calculations / Refinement description / Source and taxonomy Category: entity_src_gen / pdbx_struct_oper_list / software Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2	Sep 27, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_symmetry / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

Assembly

Deposited unit

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

Summary:

• 78.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	78,818	10
Polymers	76,495	2
Non-polymers	2,323	8
Water	10,142	563

1

A: Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase

hetero molecules

Summary:

• defined by author&software
• 158 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	157,630	20
Polymers	152,991	4
Non-polymers	4,639	16
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_455	-x-1,-y,z	1
crystal symmetry operation	3_455	-y-1/2,x+1/2,z	1
crystal symmetry operation	4_445	y-1/2,-x-1/2,z	1

Calculated values:

Buried area	27270 Å2
ΔGint	-151 kcal/mol
Surface area	43450 Å2
Method	PISA

2

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

Summary:

• defined by author&software
• 158 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	157,642	20
Polymers	152,991	4
Non-polymers	4,651	16
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_565	-x,-y+1,z	1
crystal symmetry operation	3_555	-y+1/2,x+1/2,z	1
crystal symmetry operation	4_455	y-1/2,-x+1/2,z	1

Calculated values:

Buried area	28150 Å2
ΔGint	-178 kcal/mol
Surface area	44410 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	91.262, 91.262, 171.214
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P4212

• Details: biological unit is the same as asymmetric unit.

Components

Protein , 1 types, 2 molecules A B

#1: Protein

A B Inosine-5'-monophosphate dehydrogenase / IMPDH

Details:

Mass: 38247.703 Da / Num. of mol.: 2
Mutation: 91-219 residues were deleted and replaced with SGG linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: guaB, VC_0767 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KTW3, IMP dehydrogenase

Non-polymers , 6 types, 571 molecules

#2: Chemical

A-500 B-500 ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE

Details:

Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₄O₉P

#3: Chemical

A-501 B-501 ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Details:

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

#4: Chemical

A-502 B-502 ChemComp-K / POTASSIUM ION

Details:

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

#5: Chemical

A-503 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Details:

Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃

#6: Chemical

B-503 ChemComp-PO4 / PHOSPHATE ION

Details:

Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄

#7: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.33 ų/Da / Density % sol: 47.21 %
• Crystal grow: Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 ; Details: 1.03 M sodium/phosphate buffer, 0.15 M malate, 3% PEG-300; PH range: 5

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
• Detector: Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2014
• Radiation: Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9792 Å / Relative weight: 1
• Reflection: Resolution: 1.62→50 Å / Num. all: 92477 / Num. obs: 92477 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / B_iso Wilson estimate: 29.6 Ų / R_merge(I) obs: 0.067 / R_pim(I) all: 0.025 / R_rim(I) all: 0.071 / Χ²: 1.008 / Net I/av σ(I): 27.585 / Net I/σ(I): 10.8 / Num. measured all: 754711

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Mean I/σ(I) obs	Num. unique all	CC1/2	Rpim(I) all	Rrim(I) all	Χ2	% possible all
1.62-1.65	7.8	0.743	2.84	4551	0.839	0.283	0.796	0.875	100
1.65-1.68	8.2	0.667		4564	0.878	0.248	0.712	0.893	100
1.68-1.71	8.2	0.559		4535	0.905	0.208	0.597	0.915	100
1.71-1.75	8.2	0.48		4568	0.929	0.178	0.512	0.939	100
1.75-1.78	8.2	0.376		4552	0.954	0.139	0.401	0.977	100
1.78-1.82	8.2	0.31		4577	0.965	0.115	0.331	0.989	100
1.82-1.87	8.2	0.258		4561	0.976	0.095	0.275	1.027	100
1.87-1.92	8.2	0.202		4561	0.985	0.075	0.216	1.051	100
1.92-1.98	8.2	0.167		4575	0.988	0.062	0.178	1.06	100
1.98-2.04	8.3	0.137		4598	0.992	0.051	0.146	1.088	100
2.04-2.11	8.3	0.111		4588	0.994	0.041	0.118	1.09	100
2.11-2.2	8.3	0.093		4579	0.995	0.034	0.099	1.057	100
2.2-2.3	8.3	0.08		4626	0.997	0.03	0.086	1.015	100
2.3-2.42	8.3	0.07		4617	0.997	0.026	0.075	0.966	100
2.42-2.57	8.3	0.064		4621	0.997	0.023	0.068	0.982	100
2.57-2.77	8.2	0.061		4670	0.997	0.022	0.065	1.06	100
2.77-3.05	8.2	0.064		4656	0.997	0.023	0.068	1.278	100
3.05-3.49	8.1	0.058		4700	0.997	0.022	0.062	1.247	100
3.49-4.4	7.9	0.043		4766	0.998	0.016	0.046	0.847	100
4.4-50	7.7	0.035		5012	0.995	0.014	0.038	0.783	99.5

Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
SBC-Collect		data collection
PDB_EXTRACT	3.15	data extraction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QNE

4qne

Resolution: 1.62→44.2 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.961 / SU B: 2.796 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.18157	4552	4.9 %	RANDOM
Rwork	0.152	-	-	-
obs	0.15345	87862	99.92 %	-

• 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: 23.896 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.1 Å2	-0 Å2	-0 Å2
2-	-	0.1 Å2	0 Å2
3-	-	-	-0.2 Å2

Refinement step

Cycle: LAST / Resolution: 1.62→44.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5029	0	149	563	5741

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	5474
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5395
X-RAY DIFFRACTION	r_angle_refined_deg	1.919	2.004	7485
X-RAY DIFFRACTION	r_angle_other_deg	0.863	3	12436
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.062	5	756
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.198	23.819	199
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.553	15	935
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.088	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	887
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6207
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1172
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	1.604	1.91	2828
X-RAY DIFFRACTION	r_mcbond_other	1.604	1.91	2827
X-RAY DIFFRACTION	r_mcangle_it	2.369	2.856	3546
X-RAY DIFFRACTION	r_mcangle_other	2.369	2.857	3547
X-RAY DIFFRACTION	r_scbond_it	2.491	2.307	2646
X-RAY DIFFRACTION	r_scbond_other	2.479	2.305	2643
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.825	3.332	3898
X-RAY DIFFRACTION	r_long_range_B_refined	6.011	17.241	6534
X-RAY DIFFRACTION	r_long_range_B_other	5.712	16.532	6257
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.62→1.662 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.245	323	-
Rwork	0.214	6422	-
obs	-	-	99.97 %

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	0.3955	0.0788	-0.0475	0.084	-0.0604	0.0675	0.0027	0.0351	0.0387	0.0181	-0.004	-0.0072	-0.0192	-0.007	0.0013	0.0111	-0.0014	0.0001	0.0103	0.0074	0.0092	-36.9633	26.099	22.8887
2	0.2109	0.1486	-0.0524	0.2208	-0.0028	0.1579	0.0045	-0.023	-0.0213	0.0226	-0.0047	0.0056	0.0451	-0.0056	0.0002	0.0237	-0.0115	-0.0008	0.0157	0.0064	0.0068	-17.9604	25.3234	62.5551

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 377
2	X-RAY DIFFRACTION	2	B	0 - 377