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- PDB-4af0: Crystal structure of cryptococcal inosine monophosphate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 4af0
TitleCrystal structure of cryptococcal inosine monophosphate dehydrogenase
Components(INOSINE-5'-MONOPHOSPHATE ...) x 2
KeywordsOXIDOREDUCTASE / GTP BIOSYNTHESIS / DRUG RESISTANCE
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / 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 / MYCOPHENOLIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesCRYPTOCOCCUS NEOFORMANS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsValkov, E. / Stamp, A. / Morrow, C.A. / Kobe, B. / Fraser, J.A.
CitationJournal: Plos Pathog. / Year: 2012
Title: De Novo GTP Biosynthesis is Critical for Virulence of the Fungal Pathogen Cryptococcus Neoformans
Authors: Morrow, C.A. / Valkov, E. / Stamp, A. / Chow, E.W.L. / Lee, I.R. / Wronski, A. / Williams, S.J. / Hill, J.M. / Djordjevic, J.T. / Kappler, U. / Kobe, B. / Fraser, J.A.
History
DepositionJan 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: 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 / 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 / _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. 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

Downloads & links

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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)120,2708
Polymers118,7412
Non-polymers1,5296
Water9,278515
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)240,18412
Polymers237,5094
Non-polymers2,6748
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 area24350 Å2
ΔGint-78.1 kcal/mol
Surface area54900 Å2
MethodPISA
2
B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules

B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules

B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules

B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,89620
Polymers237,4534
Non-polymers3,44316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area26050 Å2
ΔGint-200.9 kcal/mol
Surface area55020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.630, 149.630, 122.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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INOSINE-5'-MONOPHOSPHATE ... , 2 types, 2 molecules AB

#1: Protein INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE


Mass: 59377.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRYPTOCOCCUS NEOFORMANS (fungus) / Variant: GRUBII H99 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: E3P6S0, IMP dehydrogenase
#2: Protein INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE


Mass: 59363.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRYPTOCOCCUS NEOFORMANS (fungus) / Variant: GRUBII H99 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: E3P6S0, IMP dehydrogenase

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Non-polymers , 4 types, 521 molecules

#3: Chemical ChemComp-MOA / MYCOPHENOLIC ACID / 6-(1,3-DIHYDRO-7-HYDROXY-5-METHOXY-4-METHYL-1-OXOISOBENZOFURAN-6-YL)-4-METHYL-4-HEXANOIC ACID / Mycophenolic acid


Mass: 320.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20O6 / Comment: medication, immunosuppressant*YM
#4: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.89 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.9 M LITHIUM SULFATE, 0.09 M IMIDAZOLE/HCL PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→47.4 Å / Num. obs: 67847 / % possible obs: 99.1 % / Observed criterion σ(I): 1.8 / Redundancy: 5.9 % / Biso Wilson estimate: 33.48 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JCN

1jcn


Resolution: 2.2→47.44 Å / Cor.coef. Fo:Fc: 0.9422 / Cor.coef. Fo:Fc free: 0.9186 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.153 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.142
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 3429 5.05 %RANDOM
Rwork0.1733 ---
obs0.1751 67847 99.12 %-
Displacement parametersBiso mean: 40.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.4888 Å20 Å20 Å2
2--3.4888 Å20 Å2
3----6.9776 Å2
Refine analyzeLuzzati coordinate error obs: 0.244 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5909 0 102 515 6526
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016119HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.128286HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2120SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes898HARMONIC5
X-RAY DIFFRACTIONt_it6119HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion17.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion795SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7604SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2382 257 5.12 %
Rwork0.2212 4763 -
all0.2221 5020 -
obs--99.12 %
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)
11.30370.3682-0.16780.7999-0.05820.3251-0.03690.07780.0892-0.02750.0342-0.0666-0.06110.01410.0027-0.1427-0.0113-0.0162-0.1501-0.00860.138810.999424.794238.5287
20.68010.3195-0.06671.4426-0.26280.41120.0353-0.0358-0.05830.0874-0.04380.0846-0.0044-0.07130.0085-0.1651-0.0141-0.0129-0.1426-0.01610.150150.022763.822246.1175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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