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- PDB-5ahl: Apo-form of the DeltaCBS mutant of IMPDH from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5ahl
TitleApo-form of the DeltaCBS mutant of IMPDH from Pseudomonas aeruginosa
ComponentsINOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CBS MODULE / DELETION MUTANT / ALLOSTERIC REGU 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
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 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_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.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_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,7262
Polymers41,7031
Non-polymers231
Water7,386410
1
A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)333,80516
Polymers333,6218
Non-polymers1848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x,-y,-z-11
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_554-x,y,-z-11
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_554-y,-x,-z-11
Buried area27260 Å2
ΔGint-236.6 kcal/mol
Surface area95880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.837, 144.837, 116.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 41702.574 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-92,202-489
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETION MUTANT (RESIDUES 93-201)

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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: HEPES 0.1 M PH 7.5, NACL 4.3 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: 45333 / % possible obs: 100 % / Observed criterion σ(I): 1.1 / Redundancy: 14.7 % / Biso Wilson estimate: 23.01 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.9
Reflection shellResolution: 1.89→1.98 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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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: 1.951→45.476 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 2087 5 %
Rwork0.1644 --
obs0.1664 41839 92.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.5 Å2
Refinement stepCycle: LAST / Resolution: 1.951→45.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 1 410 2746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082439
X-RAY DIFFRACTIONf_angle_d1.0323306
X-RAY DIFFRACTIONf_dihedral_angle_d14.479916
X-RAY DIFFRACTIONf_chiral_restr0.042390
X-RAY DIFFRACTIONf_plane_restr0.005431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9508-1.99620.3016470.1775993X-RAY DIFFRACTION35
1.9962-2.04610.1979940.17531821X-RAY DIFFRACTION65
2.0461-2.10150.21931500.18692402X-RAY DIFFRACTION86
2.1015-2.16330.25251390.20562831X-RAY DIFFRACTION99
2.1633-2.23310.26681440.18832844X-RAY DIFFRACTION100
2.2331-2.31290.22631510.18232833X-RAY DIFFRACTION100
2.3129-2.40550.21911390.17452854X-RAY DIFFRACTION100
2.4055-2.5150.1921510.17422847X-RAY DIFFRACTION100
2.515-2.64760.21361490.17642841X-RAY DIFFRACTION100
2.6476-2.81340.23791440.18782879X-RAY DIFFRACTION100
2.8134-3.03060.23871590.18692859X-RAY DIFFRACTION100
3.0306-3.33550.19851690.1632844X-RAY DIFFRACTION100
3.3355-3.8180.16791510.12962909X-RAY DIFFRACTION100
3.818-4.80940.15221560.12272916X-RAY DIFFRACTION100
4.8094-45.48830.21241440.17523079X-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)
10.0490.00030.01910.03450.0060.0536-0.0469-0.0143-0.05360.0593-0.0039-0.04360.0359-0.0241-0.03010.16190.0030.03640.16340.05350.1724-3.8649-28.8579-33.6309
20.0095-0.00130.00290.01060.00910.014-0.00590.0191-0.0509-0.00060.02-0.01450.0463-0.0480.01020.1682-0.03450.07520.15410.0160.286-14.6004-43.7689-39.8729
30.0025-0.00350.00110.0057-0.00140.0049-0.0561-0.0725-0.05410.0533-0.01190.02090.0417-0.0486-0.03810.1389-0.06520.17710.09640.15550.0841-16.2291-26.5067-26.9426
40.0020.0017-0.00220.001-00.0011-0.01190.0341-0.00710.00960.0142-0.0280.0059-0.0157-00.1284-0.01680.03660.13660.04860.1108-2.8231-26.037-38.303
5-0.0001-0.00020.0001-0-00.0011-0.00920.00280.00970.0017-0.0065-0.0005-0.0065-0.023200.21780.02320.08990.31310.00640.1708-5.9873-26.1427-59.131
60.0105-0.00510.00850.0184-0.00230.0093-0.0435-0.0121-0.02590.0299-0.0355-0.04610.0190.0224-0.03220.1341-0.00250.00660.15290.07010.13296.7593-24.9218-30.5864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 75 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 76 THROUGH 239 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 240 THROUGH 337 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 338 THROUGH 371 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 372 THROUGH 428 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 429 THROUGH 467 )

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