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- PDB-5ahm: IMP-bound form of the DeltaCBS mutant of IMPDH from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 5ahm
TitleIMP-bound 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 / metal ion binding / identical protein binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase / GMP reductase, conserved site / 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. ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase / GMP reductase, conserved site / 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 / PHOSPHATE ION / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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
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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BC" 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
B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5769
Polymers83,4052
Non-polymers1,1717
Water10,287571
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)338,30636
Polymers333,6218
Non-polymers4,68528
Water1448
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 area49940 Å2
ΔGint-395.8 kcal/mol
Surface area90370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.600, 103.600, 158.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-2170-

HOH

21A-2212-

HOH

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Components

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


Mass: 41702.574 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-92,202-489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (unknown) / 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.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETION OF THE CBS MODULE (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: 1.9 Å3/Da / Density % sol: 34.5 % / Description: NONE
Crystal growDetails: HEPES 0.1 M PH 7.5, NH4SO4 1.26 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: 1.75→43.34 Å / Num. obs: 152733 / % possible obs: 99.5 % / Observed criterion σ(I): 1.1 / Redundancy: 3.5 % / Biso Wilson estimate: 0.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.1
Reflection shellResolution: 1.74→1.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.9 / % possible all: 98.9

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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
Resolution: 1.74→43.3 Å / SU ML: 0.2 / σ(F): 1.1 / Phase error: 19.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 7724 5.1 %
Rwork0.1608 --
obs0.1622 152733 91.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5119 0 71 571 5761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095424
X-RAY DIFFRACTIONf_angle_d1.1097373
X-RAY DIFFRACTIONf_dihedral_angle_d14.0732024
X-RAY DIFFRACTIONf_chiral_restr0.044855
X-RAY DIFFRACTIONf_plane_restr0.005956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7499-1.76980.31142400.29794664X-RAY DIFFRACTION88
1.7698-1.79060.29212700.27584737X-RAY DIFFRACTION91
1.7906-1.81240.28972260.25924723X-RAY DIFFRACTION90
1.8124-1.83540.30772890.25174569X-RAY DIFFRACTION88
1.8354-1.85950.24582200.23834429X-RAY DIFFRACTION83
1.8595-1.8850.2342370.22134449X-RAY DIFFRACTION85
1.885-1.91190.25462220.21874946X-RAY DIFFRACTION93
1.9119-1.94050.26842480.20274835X-RAY DIFFRACTION93
1.9405-1.97080.23552390.19314962X-RAY DIFFRACTION93
1.9708-2.00310.22172850.19244911X-RAY DIFFRACTION93
2.0031-2.03770.24352830.18844842X-RAY DIFFRACTION93
2.0377-2.07470.21232920.17664945X-RAY DIFFRACTION93
2.0747-2.11460.19922520.16984901X-RAY DIFFRACTION93
2.1146-2.15780.22272770.16834882X-RAY DIFFRACTION93
2.1578-2.20470.19962470.15874788X-RAY DIFFRACTION91
2.2047-2.2560.18152240.16114515X-RAY DIFFRACTION86
2.256-2.31240.18532900.16354495X-RAY DIFFRACTION87
2.3124-2.37490.19832510.15754956X-RAY DIFFRACTION95
2.3749-2.44480.19172780.16114970X-RAY DIFFRACTION95
2.4448-2.52370.20392780.15394996X-RAY DIFFRACTION95
2.5237-2.61390.19652450.1554935X-RAY DIFFRACTION94
2.6139-2.71850.17962590.15585017X-RAY DIFFRACTION95
2.7185-2.84220.18452940.16415001X-RAY DIFFRACTION95
2.8422-2.9920.21122450.16884609X-RAY DIFFRACTION88
2.992-3.17940.18762630.1644842X-RAY DIFFRACTION93
3.1794-3.42480.17452880.15055064X-RAY DIFFRACTION96
3.4248-3.76930.15562540.1334976X-RAY DIFFRACTION95
3.7693-4.31430.14112740.12325130X-RAY DIFFRACTION97
4.3143-5.43390.16722050.13214886X-RAY DIFFRACTION93
5.4339-43.35790.16382490.16825034X-RAY DIFFRACTION95
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)
10.1447-0.0251-0.11050.05090.03860.0161-0.00290.0212-0.01410.0384-0.0027-0.0241-0.0026-0.033600.1080.00280.00910.10570.02460.1401-20.9283-14.11254.9284
20.0016-0.00670.00230.00610.0130.02580.12130.2587-0.1495-0.0814-0.15740.13590.0130.007300.0890.0236-0.04690.1761-0.04780.1912-40.0548-16.4005-8.1522
30.0348-0.02070.02480.140.01340.10420.04120.00710.00080.0342-0.02850.0236-0.0246-0.0012-00.07580.00450.02160.10110.00550.1495-31.4612-3.4395.443
40.010.0143-0.00350.03560.01070.00620.11330.0168-0.0388-0.0764-0.0191-0.01910.06-0.056700.14990.04010.02250.1440.00060.0835-23.8873-9.8103-13.8736
50.06550.03530.01320.01070.00470.0241-0.02090.0614-0.03340.00890.0211-0.0908-0.091-0.0019-00.15010.01280.03030.1552-0.00680.1243-21.227-12.0655-8.5323
60.0261-0.04050.01760.0086-0.0042-0.0125-0.03270.1110.0033-0.00560.0497-0.05270.1059-0.0216-00.0857-0.0010.01760.13980.03910.1138-9.0262-16.59820.2721
70.05930.02780.03990.12640.03530.05820.0233-0.02050.0013-0.0285-0.02080.03440.03380.014400.16-0.0126-0.04090.16850.00430.1131-15.9001-19.7916-53.2331
8-0.0103-0.0028-0.0132-0.0107-0.00950.0105-0.0503-0.1333-0.00810.1646-0.17390.18690.1709-0.0383-00.3009-0.13380.0244-0.11050.5239-0.1775-17.979-38.318-39.4598
9-0.0014-0.0098-0.020.03580.0350.02050.0155-0.0933-0.11520.02190.025-0.01080.19780.1002-00.3029-0.0107-0.0530.170.01780.2497-8.0769-41.3449-51.0214
100.05340.0216-0.01770.0149-0.06890.0416-0.0033-0.0319-0.0471-0.04680.0577-0.0018-0.0086-0.0137-00.1935-0.0176-0.03380.1696-0.02130.1217-7.2476-24.9259-54.9577
110.0002-0.00040.00710.01950.0041-0.00090.0891-0.20990.0238-0.10870.02150.0583-0.027-0.0136-00.1854-0.0596-0.07390.3360.0218-0.0267-12.2467-22.9565-34.2663
120.003-0.00380.0086-0.0019-0.00430.00520.01810.0042-0.00580.0061-0.0279-0.07460.01260.0202-00.3234-0.0203-0.03890.521-0.02950.1986-6.0821-22.9993-33.7435
130.00040.00260.00410.00270.00060.0008-0.0374-0.05620.03620.0168-0.0870.10620.006-0.052500.2205-0.02580.00810.2241-0.01070.1806-24.7314-16.4849-45.6058
140.0138-0.0225-0.0110.0137-0.009-0.00460.04730.0251-0.03210.1322-0.0730.1499-0.063-0.081-00.243-0.0093-0.01430.15450.01140.0842-17.45-7.1377-47.8408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 54 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 55 THROUGH 217 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 218 THROUGH 352 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 353 THROUGH 385 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 386 THROUGH 447 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 448 THROUGH 487 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 1 THROUGH 54 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 55 THROUGH 210 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 211 THROUGH 266 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 267 THROUGH 352 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 353 THROUGH 385 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 386 THROUGH 428 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 429 THROUGH 447 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 448 THROUGH 487 )

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