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- PDB-4ix2: Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, dele... -

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Basic information

Entry
Database: PDB / ID: 4ix2
TitleInosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, complexed with IMP
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / structural genomics / IMPDH / IMP / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
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
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 ...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
Similarity search - Domain/homology
INOSINIC ACID / : / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.146 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, complexed with IMP.
Authors: Osipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 6, 2013ID: 4FF0
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...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 ..._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_seq_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

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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
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,54012
Polymers152,9914
Non-polymers1,5498
Water15,727873
1
A: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,54012
Polymers152,9914
Non-polymers1,5498
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area20680 Å2
ΔGint-117 kcal/mol
Surface area44630 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,54012
Polymers152,9914
Non-polymers1,5498
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area20480 Å2
ΔGint-111 kcal/mol
Surface area44720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.180, 167.158, 93.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-722-

HOH

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Components

#1: Protein
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


Mass: 38247.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: guaB, VC0767, VC_0767 / 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.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 873 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 91-219 ARE DELETED AND REPLACED WITH 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.86 sodium/potassium buffer, 0.15 M MOPS buffer, 0.02 M sodium fluoride, 0.01 M IMP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.5
ReflectionResolution: 2.15→38.1 Å / Num. all: 71185 / Num. obs: 71185 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.195 / Χ2: 1.498 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.15-2.196.70.9212.6635180.95499.5
2.19-2.237.20.88735120.98100
2.23-2.277.30.81634920.978100
2.27-2.327.30.76335481.004100
2.32-2.377.40.66235061.014100
2.37-2.427.40.60135531.037100
2.42-2.487.40.51734981.064100
2.48-2.557.40.4635571.098100
2.55-2.627.40.42535351.123100
2.62-2.717.40.37435221.164100
2.71-2.817.40.31735491.24100
2.81-2.927.40.25535651.355100
2.92-3.057.40.21335431.459100
3.05-3.217.40.18335691.596100
3.21-3.417.40.13835561.816100
3.41-3.687.30.11835842.129100
3.68-4.057.20.09835782.412100
4.05-4.637.10.08835942.737100
4.63-5.8370.08136512.329100
5.83-506.70.06837552.599.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FEZ
Resolution: 2.146→38.1 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.7734 / σ(F): 1.34 / σ(I): 0 / Phase error: 28.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3606 5.07 %Random
Rwork0.2077 ---
obs0.2114 71179 99.69 %-
all-71179 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.45 Å2 / Biso mean: 27.3149 Å2 / Biso min: 0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.146→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 96 873 10707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039971
X-RAY DIFFRACTIONf_angle_d0.70713490
X-RAY DIFFRACTIONf_chiral_restr0.0431589
X-RAY DIFFRACTIONf_plane_restr0.0031744
X-RAY DIFFRACTIONf_dihedral_angle_d13.5563652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.1466-2.18360.33231660.227431913357335790
2.1836-2.22330.30071550.23193369352496
2.2233-2.26610.26921920.22173321351395
2.2661-2.31230.32581630.22673362352595
2.3123-2.36260.26511740.22593369354395
2.3626-2.41750.29461860.22173357354395
2.4175-2.4780.27061720.2213355352795
2.478-2.54490.27441740.21793376355095
2.5449-2.61980.21971970.22173354355194
2.6198-2.70440.28891990.21383337353694
2.7044-2.8010.26841970.2113347354494
2.801-2.91310.29762020.20993366356894
2.9131-3.04560.241760.20423381355795
3.0456-3.20610.25831900.20573394358495
3.2061-3.40680.24831770.19433380355795
3.4068-3.66960.2581680.18283421358995
3.6696-4.03850.20461940.18413385357995
4.0385-4.62180.21991570.17883448360596
4.6218-5.81910.23711950.20293460365595
5.8191-36.29020.32061680.25633599376795
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)
10.0155-0.03630.01360.1189-0.00990.2084-0.03370.02590.0105-0.0063-0.0378-0.00910.2146-0.1037-0.11380.1347-0.07170.0066-0.019-0.03930.059831.418616.124561.7082
20.02960.0309-0.05380.0762-0.03130.14070.050.01370.02460.0191-0.02910.0111-0.1717-0.03360.00340.13680.02620.03040.02270.00830.085830.940267.370413.7447
30.0546-0.0563-0.0230.0904-0.00580.05630.0058-0.0568-0.028-0.00080.01750.0470.0079-0.13140.01240.0264-0.0325-0.01530.14030.00410.072716.207230.874513.7022
40.0646-0.0072-0.05450.04760.02090.1385-0.01470.0037-0.0107-0.04130.0082-0.0026-0.1202-0.22740.0160.03640.0659-0.0140.1757-0.03460.093516.089652.26661.78
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:487)A3 - 487
2X-RAY DIFFRACTION2chain 'B' and (resseq 4:487)B4 - 487
3X-RAY DIFFRACTION3chain 'C' and (resseq 4:486)C4 - 486
4X-RAY DIFFRACTION4chain 'D' and (resseq 3:486)D3 - 486

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