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- PDB-5ahn: IMP-bound form of the D199N mutant of IMPDH from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 5ahn
TitleIMP-bound form of the D199N mutant of IMPDH from Pseudomonas aeruginosa
ComponentsINOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CBS MODULE / POINT MUTANT / ALLOSTERIC REGULATION NUCLEOTIDE METABOLISM
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
INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å
AuthorsLabesse, G. / Alexandre, T. / Gelin, M. / Haouz, A. / Munier-Lehmann, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystallographic Studies of Two Variants of Pseudomonas Aeruginosa Impdh with Impaired Allosteric Regulation
Authors: Labesse, G. / Alexandre, T. / Gelin, M. / Haouz, A. / Munier-Lehmann, H.
History
DepositionFeb 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,1634
Polymers51,7661
Non-polymers3973
Water6,125340
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)208,65316
Polymers207,0654
Non-polymers1,58712
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 area13970 Å2
ΔGint-165.6 kcal/mol
Surface area42600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.551, 116.551, 58.247
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: 51766.371 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXM5, IMP dehydrogenase
#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPOINT MUTATION D199N

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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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: PEG 4000 10%, MES 0.1 M PH 7, MGCL2 0.2 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.65→82.2 Å / Num. obs: 46336 / % possible obs: 98.6 % / Observed criterion σ(I): 1.1 / Redundancy: 3.5 % / Biso Wilson estimate: 23.447 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DQW

4dqw


Resolution: 1.652→36.857 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 2284 5 %
Rwork0.1612 --
obs0.1622 45339 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.3 Å2
Refinement stepCycle: LAST / Resolution: 1.652→36.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 25 340 2499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112301
X-RAY DIFFRACTIONf_angle_d1.623132
X-RAY DIFFRACTIONf_dihedral_angle_d12.99853
X-RAY DIFFRACTIONf_chiral_restr0.053376
X-RAY DIFFRACTIONf_plane_restr0.007405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6516-1.68750.2493820.23291460X-RAY DIFFRACTION53
1.6875-1.72670.22521300.22782558X-RAY DIFFRACTION93
1.7267-1.76990.25331580.21732776X-RAY DIFFRACTION100
1.7699-1.81780.2251410.20072782X-RAY DIFFRACTION100
1.8178-1.87130.20961390.18142740X-RAY DIFFRACTION100
1.8713-1.93170.1791370.17552783X-RAY DIFFRACTION100
1.9317-2.00070.21061560.17292790X-RAY DIFFRACTION100
2.0007-2.08080.19571460.1622794X-RAY DIFFRACTION100
2.0808-2.17550.16131460.15652745X-RAY DIFFRACTION100
2.1755-2.29020.18791520.15212785X-RAY DIFFRACTION100
2.2902-2.43360.17561280.15522795X-RAY DIFFRACTION100
2.4336-2.62150.17341620.16222767X-RAY DIFFRACTION100
2.6215-2.88520.18911460.16142804X-RAY DIFFRACTION100
2.8852-3.30250.17221790.15892756X-RAY DIFFRACTION100
3.3025-4.15990.1551360.13812854X-RAY DIFFRACTION100
4.1599-36.86580.17611460.15552866X-RAY DIFFRACTION100
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)
10.01440.00030.00240.0078-0.00550.0066-0.0131-0.05850.03380.0177-0.0115-0.0211-0.01510.0007-0-0.03730.0760.12640-0.1148-0.0151-9.432732.693730.7596
20.00590.0043-0.00140.00390.00340.003-0.00450.00380.0298-0.00250.00140.03320.0096-0.019500.05880.0166-0.00280.05660.01320.0677-22.446727.623124.8309
30.01210.00450.0017-0.00190.0016-0.00210.0268-0.0632-0.0077-0.01240.0484-0.0389-0.01310.008-0-0.06230.00390.12740.0210.0165-0.2097-3.245223.711627.3212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 223 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 224 THROUGH 305 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 306 THROUGH 467 )

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