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

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Basic information

Entry
Database: PDB / ID: 4qne
TitleInosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with NAD and IMP
ComponentsInosine 5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / 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 and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase/GMP reductase / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase/GMP reductase / 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
Similarity search - Domain/homology
INOSINIC ACID / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsOsipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: 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
DepositionJun 17, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionAug 6, 2014ID: 4HLV
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine 5'-monophosphate dehydrogenase
B: Inosine 5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5978
Polymers76,4952
Non-polymers2,1016
Water3,207178
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


Theoretical massNumber of molelcules
Total (without water)314,38732
Polymers305,9828
Non-polymers8,40624
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area57380 Å2
ΔGint-276 kcal/mol
Surface area82140 Å2
MethodPISA
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 number90
Space group name H-MP4212

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Components

#1: Protein Inosine 5'-monophosphate dehydrogenase


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 (unknown)
Strain: N16961 / Gene: VC0767 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KTW3, IMP dehydrogenase
#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 91-219 ARE DELETED AND REPLACED WITH AN SGG LINKER.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 20, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 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 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.319-2.366.60.9182.11100
2.36-2.46.80.8211100
2.4-2.457.20.7321100
2.45-2.57.60.6091100
2.5-2.558.10.5381100
2.55-2.618.90.5261100
2.61-2.689.10.4161100
2.68-2.759.10.4141100
2.75-2.839.10.2981100
2.83-2.929.20.2561100
2.92-3.039.20.213199.9
3.03-3.159.20.1741100
3.15-3.299.30.1331100
3.29-3.479.40.1011100
3.47-3.689.50.0841100
3.68-3.979.50.0691100
3.97-4.379.50.0611100
4.37-59.40.056199.9
5-6.299.30.0571100
6.29-508.50.056199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FO4
Resolution: 2.32→47.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.27019 1553 5 %RANDOM
Rwork0.1963 ---
obs0.2 29325 99.04 %-
all-30878 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.852 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0 Å20 Å2
2---1.48 Å2-0 Å2
3---2.95 Å2
Refinement stepCycle: LAST / Resolution: 2.32→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 136 178 5298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195325
X-RAY DIFFRACTIONr_bond_other_d0.0030.025200
X-RAY DIFFRACTIONr_angle_refined_deg1.8522.0027251
X-RAY DIFFRACTIONr_angle_other_deg0.874311957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78123.769199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36115887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8411539
X-RAY DIFFRACTIONr_chiral_restr0.10.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6093.1992764
X-RAY DIFFRACTIONr_mcbond_other2.6013.1982763
X-RAY DIFFRACTIONr_mcangle_it3.7764.7863456
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1693.6512561
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.319→2.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 94 -
Rwork0.256 2152 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.52220.07-0.06150.1944-0.19160.22060.0022-0.01730.01860.0573-0.0325-0.0624-0.02540.05370.03030.0808-0.0251-0.05190.1232-0.02630.058985.911411.456514.4806
20.2757-0.08470.00830.4839-0.08230.510.06990.06670.0297-0.03090.00810.0022-0.18230.1049-0.07810.21-0.05640.06440.0814-0.00040.029871.358525.6033-32.2321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 503
2X-RAY DIFFRACTION2B5 - 503

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