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- PDB-3zfh: Crystal structure of Pseudomonas aeruginosa inosine 5'-monophosph... -

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Basic information

Entry
Database: PDB / ID: 3zfh
TitleCrystal structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase
ComponentsINOSINE 5'-MONOPHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / GUANINE NUCLEOTIDE BIOSYNTHESIS
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / ATP binding / identical protein 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
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRao, V.A. / Shepherd, S.M. / Owen, R. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of Pseudomonas Aeruginosa Inosine 5'-Monophosphate Dehydrogenase
Authors: Rao, V.A. / Shepherd, S.M. / Owen, R. / Hunter, W.N.
History
DepositionDec 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INOSINE 5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2152
Polymers54,1801
Non-polymers351
Water2,108117
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


Theoretical massNumber of molelcules
Total (without water)216,8618
Polymers216,7204
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11960 Å2
ΔGint-118.7 kcal/mol
Surface area43080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.546, 115.546, 56.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein INOSINE 5'-MONOPHOSPHATE DEHYDROGENASE / IMP DEHYDROGENASE / IMPD / IMPDH


Mass: 54179.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Plasmid: PET15BTEV_GUAB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9HXM5, IMP dehydrogenase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM ACETATE, 40 % 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Jan 26, 2012 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 16612 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.3
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.3 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TSB

3tsb


Resolution: 2.25→81.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.779 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. RESIDUES 92-204, 371-425 AND 468-489 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19024 844 5.1 %RANDOM
Rwork0.14782 ---
obs0.15003 15768 93.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.935 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2---2.15 Å20 Å2
3---4.29 Å2
Refinement stepCycle: LAST / Resolution: 2.25→81.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 1 117 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9672987
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10124.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86615381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6821516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211615
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 51 -
Rwork0.186 1181 -
obs--96.1 %
Refinement TLS params.

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

IDL11 (°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)
10.95410.76370.16561.96370.25310.44550.08410.0323-0.11480.1457-0.0079-0.30320.04710.0662-0.07620.06130.0071-0.00040.0602-0.01070.064927.6774.676-25.904
21.72141.99470.28484.69191.28332.06310.11610.0141-0.19020.30110.0119-0.5558-0.00810.2031-0.1280.0534-0.0304-0.06010.099-0.03350.146240.08619.627-19.543
32.31170.89410.18733.02280.23530.4798-0.06930.1033-0.0746-0.10790.0205-0.1551-0.17990.03940.04880.1258-0.02380.01580.14320.00980.036826.58421.588-32.013
40.70940.23910.29922.14790.0820.30540.02180.0053-0.11630.05970.0041-0.15330.0420.0848-0.02590.0754-0.01210.00490.0921-0.01290.062223.5913.467-26.177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 70
2X-RAY DIFFRACTION2A71 - 245
3X-RAY DIFFRACTION3A246 - 304
4X-RAY DIFFRACTION4A305 - 465

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