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- PDB-2qr6: Crystal structure of IMP dehydrogenase/GMP reductase-like protein... -

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Basic information

Entry
Database: PDB / ID: 2qr6
TitleCrystal structure of IMP dehydrogenase/GMP reductase-like protein (NP_599840.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 1.50 A resolution
ComponentsIMP dehydrogenase/GMP reductase
KeywordsOXIDOREDUCTASE / NP_599840.1 / IMP dehydrogenase/GMP reductase-like protein / GMP reductase domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Inosine monophosphate dehydrogenase (IMPDH) / IMP dehydrogenase-related 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Ribbon / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel ...Inosine monophosphate dehydrogenase (IMPDH) / IMP dehydrogenase-related 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Ribbon / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMP dehydrogenase/GMP reductase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of IMP dehydrogenase/GMP reductase-like protein (NP_599840.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. AUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS WITH EBI/PISA SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 400 COMPOUND A CYSTINE REQUIRED FOR INOSITOL-5-MONOPHOSPHATE DEHYDROGENASE ACTIVITY IS ABSENT AT A ... COMPOUND A CYSTINE REQUIRED FOR INOSITOL-5-MONOPHOSPHATE DEHYDROGENASE ACTIVITY IS ABSENT AT A PUTATIVE ACTIVE SITE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS PARTIALLY REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CRYSTAL CONTAINED A MIXTURE OF BOTH CLEAVED AND UNCLEAVED FORMS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMP dehydrogenase/GMP reductase


Theoretical massNumber of molelcules
Total (without water)42,5501
Polymers42,5501
Non-polymers00
Water5,134285
1
A: IMP dehydrogenase/GMP reductase

A: IMP dehydrogenase/GMP reductase

A: IMP dehydrogenase/GMP reductase

A: IMP dehydrogenase/GMP reductase


Theoretical massNumber of molelcules
Total (without water)170,2014
Polymers170,2014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.130, 127.130, 54.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsCRYSTAL PACKING ANALYSIS WITH EBI/PISA SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase C terminus / IMP dehydrogenase / GMP reductase domain


Mass: 42550.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025 / Gene: NP_599840.1, guaB3, Cgl0604, cg0700 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8NSR4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 0.2M Mg(OAc)2, 30.0% MPD, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97925, 0.97904
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 20, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979251
30.979041
ReflectionResolution: 1.5→29.656 Å / Num. obs: 69856 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.377 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 10.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.6051.41860512226194.3
1.55-1.620.4631.82385515215198.1
1.62-1.690.3612.32029012770198.3
1.69-1.780.263.22189013717198.4
1.78-1.890.1784.72162213354198.4
1.89-2.040.1057.62235913833198.2
2.04-2.240.06511.62158713149198
2.24-2.560.04416.22252413399198.1
2.56-3.230.02823.32356513684198.1
3.23-29.6560.01934.22372113294196.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.656 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.875 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.062
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUES 178-182 AND 322-325 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. THERE ARE SOME UNMODELED DENSITIES NEAR RESIDUES 20, 26, 137, 145, 159, 184, 208, 266.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3530 5.1 %RANDOM
Rwork0.169 ---
obs0.17 69848 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 0 285 3012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222937
X-RAY DIFFRACTIONr_bond_other_d0.0040.021930
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9524031
X-RAY DIFFRACTIONr_angle_other_deg1.45934735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4725417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36423.443122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97215472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5831523
X-RAY DIFFRACTIONr_chiral_restr0.0870.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023395
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02599
X-RAY DIFFRACTIONr_nbd_refined0.1920.2560
X-RAY DIFFRACTIONr_nbd_other0.1630.22003
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21450
X-RAY DIFFRACTIONr_nbtor_other0.0770.21544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.224
X-RAY DIFFRACTIONr_mcbond_it2.24632113
X-RAY DIFFRACTIONr_mcbond_other0.5213788
X-RAY DIFFRACTIONr_mcangle_it353072
X-RAY DIFFRACTIONr_scbond_it4.98181115
X-RAY DIFFRACTIONr_scangle_it6.55111934
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 260 -
Rwork0.28 4851 -
obs-5111 98.18 %
Refinement TLS params.Method: refined / Origin x: 22.383 Å / Origin y: 16.989 Å / Origin z: 9.229 Å
111213212223313233
T-0.0831 Å2-0.024 Å2-0.0113 Å2--0.0984 Å20.0051 Å2---0.1534 Å2
L0.6857 °20.1241 °2-0.2263 °2-0.8748 °2-0.3397 °2--0.8391 °2
S-0.0179 Å °0.0355 Å °-0.0285 Å °-0.1538 Å °-0.0036 Å °-0.0343 Å °0.0409 Å °0.094 Å °0.0214 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-5 - 17714 - 196
2X-RAY DIFFRACTION1AA183 - 321202 - 340
3X-RAY DIFFRACTION1AA326 - 374345 - 393

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