PDB-5upv: Crystal Structure of the Catalytic Domain of the Inosine Monophos...

Basic information

• Entry: Database: PDB / ID: 5upv
• Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis In the presence of G36
• Components: Inosine-5'-monophosphate dehydrogenase
• Keywords: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IMPDH / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

Function / homology

Function:

XMP biosynthetic process / IMP catabolic process / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / peptidoglycan-based cell wall / nucleotide binding / metal ion binding / plasma membrane / 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:

Chem-8KV / FORMIC ACID / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase

• Biological species: Mycobacterium tuberculosis (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
• Authors: Kim, Y. / Maltseva, N. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		United States

• Citation: Journal: To Be Published; Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis In the presence of G36; Authors: Kim, Y. / Maltseva, N. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Feb 4, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 12, 2017	Group: Other
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: Inosine-5'-monophosphate dehydrogenase

hetero molecules

Summary:

• 42.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	42,652	9
Polymers	41,643	1
Non-polymers	1,010	8
Water	2,864	159

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
• 171 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	170,610	36
Polymers	166,570	4
Non-polymers	4,039	32
Water	72	4

Symmetry operations:

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

Calculated values:

Buried area	28560 Å2
ΔGint	-86 kcal/mol
Surface area	43560 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	88.128, 88.128, 84.364
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

Components

Protein , 1 types, 1 molecules A

#1: Protein

A Inosine-5'-monophosphate dehydrogenase / IMPDH / IMPDH2

Details:

Mass: 41642.621 Da / Num. of mol.: 1
Mutation: the CBS domain (residues 126-252) is replaced with GGLLV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: guaB, guaB2, Rv3411c, MTCY78.17 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BM21(DE3) magic / References: UniProt: P9WKI7, IMP dehydrogenase

Non-polymers , 5 types, 167 molecules

#2: Chemical

A-601 ChemComp-IMP / INOSINIC ACID

Details:

Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₄O₈P

#3: Chemical

A-602 ChemComp-8KV / N-{(1S)-1-[3-methoxy-4-(1,3-oxazol-5-yl)phenyl]ethyl}-N'-phenylurea

Details:

Mass: 337.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₁₉N₃O₃

#4: Chemical

A-603 A-605 A-608 ChemComp-FMT / FORMIC ACID

Details:

Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH₂O₂

#5: Chemical

A-604 A-606 A-607 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.97 ų/Da / Density % sol: 37.46 %
• Crystal grow: Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 ; Details: 0.2 M sodium chloride, 0.1 M HEPES pH 7.5, 10 % (v/v) isopropanol

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
• Detector: Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2016
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97932 Å / Relative weight: 1
• Reflection: Resolution: 1.63→50 Å / Num. obs: 39240 / % possible obs: 97.6 % / Redundancy: 5.1 % / R_sym value: 0.095 / Net I/σ(I): 16.1
• Reflection shell: Resolution: 1.63→1.66 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1628 / CC_1/2: 0.412 / R_sym value: 0.788 / % possible all: 81

Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing

Refinement

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

4zqr

Resolution: 1.63→35.708 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.1839	1866	4.78 %	random
Rwork	0.163	-	-	-
obs	0.164	39031	97.1 %	-

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.63→35.708 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2498	0	69	159	2726

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2641
X-RAY DIFFRACTION	f_angle_d	0.895	3591
X-RAY DIFFRACTION	f_dihedral_angle_d	11.242	1593
X-RAY DIFFRACTION	f_chiral_restr	0.057	430
X-RAY DIFFRACTION	f_plane_restr	0.006	466

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.6301-1.6741	0.3352	130	0.3079	2381	X-RAY DIFFRACTION	81
1.6741-1.7234	0.3337	164	0.293	2655	X-RAY DIFFRACTION	92
1.7234-1.779	0.2339	116	0.2441	2924	X-RAY DIFFRACTION	99
1.779-1.8426	0.2746	117	0.2196	2913	X-RAY DIFFRACTION	98
1.8426-1.9164	0.223	148	0.1966	2937	X-RAY DIFFRACTION	100
1.9164-2.0036	0.2096	138	0.1733	2938	X-RAY DIFFRACTION	100
2.0036-2.1092	0.2049	165	0.1603	2900	X-RAY DIFFRACTION	100
2.1092-2.2413	0.1985	143	0.1563	2924	X-RAY DIFFRACTION	99
2.2413-2.4144	0.189	124	0.1561	2949	X-RAY DIFFRACTION	100
2.4144-2.6573	0.1821	154	0.1539	2926	X-RAY DIFFRACTION	100
2.6573-3.0416	0.1586	143	0.1594	2925	X-RAY DIFFRACTION	99
3.