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- PDB-4r7j: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase with ... -

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Basic information

Entry
Database: PDB / ID: 4r7j
TitleCrystal Structure of Inosine 5'-monophosphate Dehydrogenase with the Internal Deletion Containing CBS Domain from Campylobacter jejuni
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / alpha-beta structure / hydrolase
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide 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 speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1172 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published / Year: 2014
Title: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase with the Internal Deletion Containing CBS Domain from Campylobacter jejuni
Authors: Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references / Structure summary
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,9749
Polymers41,0531
Non-polymers9218
Water2,126118
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)167,89836
Polymers164,2134
Non-polymers3,68532
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area25900 Å2
ΔGint-281 kcal/mol
Surface area50560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.413, 119.413, 69.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-501-

CL

21A-659-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Inosine-5'-monophosphate dehydrogenase


Mass: 41053.176 Da / Num. of mol.: 1 / Fragment: IMPDH-delta-S-CBS / Mutation: CBS domain (residues 92-195) is replaced with G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: guaB, Cj1058c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: Q0P9J4, IMP dehydrogenase

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Non-polymers , 7 types, 126 molecules

#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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M lithium sulfate monohydrate,0.1 M MES pH 6.0, 35 %(v/v) 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.117→50 Å / Num. all: 29178 / Num. obs: 29178 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 38.68 Å2 / Rsym value: 0.081 / Net I/σ(I): 33.7
Reflection shellResolution: 2.117→2.16 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 1434 / Rsym value: 0.746 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 4FO4

4fo4


Resolution: 2.1172→42.219 Å / SU ML: 0.19 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 1480 5.08 %random
Rwork0.173 ---
all0.174 29178 --
obs0.174 29145 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 2.1172→42.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 54 118 2833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032766
X-RAY DIFFRACTIONf_angle_d0.7023732
X-RAY DIFFRACTIONf_dihedral_angle_d13.6511035
X-RAY DIFFRACTIONf_chiral_restr0.025432
X-RAY DIFFRACTIONf_plane_restr0.002472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1172-2.18550.21831410.192424592600100
2.1855-2.26360.23461210.191724872608100
2.2636-2.35430.21361180.184724682586100
2.3543-2.46140.20791500.192424702620100
2.4614-2.59120.21071250.192524942619100
2.5912-2.75350.23991310.189324832614100
2.7535-2.9660.20811460.197524832629100
2.966-3.26440.23141510.186124992650100
3.2644-3.73650.2071400.169825422682100
3.7365-4.70660.161270.142425722699100
4.7066-42.22720.20881300.16832708283899
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)
10.31370.2176-0.43430.84750.30730.6811-0.0142-0.03980.0491-0.03530.03780.0723-0.0084-0.026900.22730.0026-0.02140.25550.02910.304939.792714.491126.4285
20.1586-0.1876-0.2560.61060.43550.7293-0.0570.5317-0.0078-0.60690.10540.2329-0.023-0.28290.00180.4490.0432-0.09430.42160.13820.32636.452833.24449.5443
30.1938-0.148-0.21630.18890.18350.58180.01420.10460.2656-0.250.00340.1862-0.2748-0.1099-00.39730.0698-0.03930.37740.0920.423736.327537.910717.6586
40.8354-0.19090.14960.77730.26420.25020.01220.01390.0286-0.00550.03060.01590.0076-0.050700.29350.01520.00280.2780.03980.302147.995826.548725.5572
50.08790.0654-0.03610.1197-0.08320.05970.09240.5668-0.4978-0.64940.0274-0.0096-0.16160.09910.00020.72330.0305-0.03220.663-0.02840.313745.767720.3265-1.7697
60.4026-0.56410.1790.93620.05320.82730.09290.1153-0.0289-0.3641-0.13920.0826-0.09280.10230.00220.4080.0154-0.06980.34070.03020.283444.866919.240510.7234
70.67680.35560.21690.4804-0.25870.36180.06830.3617-0.0159-0.2629-0.0266-0.11740.1858-0.0265-00.45440.0029-0.04450.47390.0380.437740.90493.992219.7692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 204 )
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 361 )
5X-RAY DIFFRACTION5chain 'A' and (resid 362 through 382 )
6X-RAY DIFFRACTION6chain 'A' and (resid 383 through 441 )
7X-RAY DIFFRACTION7chain 'A' and (resid 442 through 481 )

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