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- PDB-3kgy: Crystal structure of Putative dihydrofolate reductase (YP_0016360... -

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Basic information

Entry
Database: PDB / ID: 3kgy
TitleCrystal structure of Putative dihydrofolate reductase (YP_001636057.1) from CHLOROFLEXUS AURANTIACUS J-10-FL at 1.50 A resolution
ComponentsBifunctional deaminase-reductase domain protein
KeywordsOXIDOREDUCTASE / Putative dihydrofolate reductase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / nucleotide binding
Similarity search - Function
: / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Bifunctional deaminase-reductase domain protein
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative dihydrofolate reductase (YP_001636057.1) from CHLOROFLEXUS AURANTIACUS J-10-FL at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional deaminase-reductase domain protein
B: Bifunctional deaminase-reductase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,88524
Polymers53,2062
Non-polymers2,67922
Water10,196566
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.231, 57.352, 140.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUGGESTS A HEXAMER AS A OLIGOMERIZATION STATE IN SOLUTION. CRYSTAL PACKING SUPPORTS THE ASSIGNMENT A MONOMER OR DIMER.

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Components

#1: Protein Bifunctional deaminase-reductase domain protein


Mass: 26602.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus J-10-fl (bacteria)
Strain: ATCC 29366 / DSM 635 / J-10-fl / Gene: Caur_2460 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A9WHX7
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20.0000% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, 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: 0.91837,0.97922,0.97876
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979221
30.978761
ReflectionResolution: 1.5→29.709 Å / Num. obs: 72017 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.52 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.543.60.5680.91854051890.56898.7
1.54-1.583.60.441.71816950780.4498.8
1.58-1.633.60.3582.11780649960.35899
1.63-1.683.60.3132.41718548070.31399.1
1.68-1.733.60.2712.51679046930.27199.1
1.73-1.793.60.2183.41633845480.21899.3
1.79-1.863.60.184.11583143970.1899.5
1.86-1.943.60.1831.11523542550.18399.7
1.94-2.023.60.1322.71485440950.13299.8
2.02-2.123.60.1262.21418339250.12699.6
2.12-2.243.70.0996.71365437110.09999.6
2.24-2.373.70.1083.41287335250.10899.6
2.37-2.543.70.0857.51239033550.08599.9
2.54-2.743.70.0835.21149531290.08399.9
2.74-33.70.0688.91060528800.068100
3-3.353.70.0629.4970026400.062100
3.35-3.873.60.0627.3849423370.062100
3.87-4.743.60.05311720920050.05399.9
4.74-6.713.50.05510.4551415680.05599.6
6.71-29.713.30.0599.729208840.05996.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.709 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.277 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.068
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.NADPH MOLECULEs FROM BACTERIAL NATURAL PROCESSING AND CHLORIDE IONS FROM CRYSTALLIZATION ARE MODELED IN THE STRUCTURE. ETHYLENE GLYCOL MOLECULES FROM CRYOPROTECTANT ARE ALSO MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.174 3626 5 %RANDOM
Rwork0.149 ---
obs0.15 71950 99.2 %-
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 max: 64.38 Å2 / Biso mean: 19.867 Å2 / Biso min: 5.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 170 566 4206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224038
X-RAY DIFFRACTIONr_bond_other_d0.0040.022830
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9895503
X-RAY DIFFRACTIONr_angle_other_deg1.31836824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1735500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36922.553188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98315632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.821539
X-RAY DIFFRACTIONr_chiral_restr0.0990.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024589
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02878
X-RAY DIFFRACTIONr_nbd_refined0.2310.3772
X-RAY DIFFRACTIONr_nbd_other0.1990.33174
X-RAY DIFFRACTIONr_nbtor_refined0.1850.51985
X-RAY DIFFRACTIONr_nbtor_other0.0890.52045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5789
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.380
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.561
X-RAY DIFFRACTIONr_mcbond_it1.92932819
X-RAY DIFFRACTIONr_mcbond_other0.4573960
X-RAY DIFFRACTIONr_mcangle_it2.28953841
X-RAY DIFFRACTIONr_scbond_it3.9781877
X-RAY DIFFRACTIONr_scangle_it5.088111662
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 232 -
Rwork0.212 4950 -
all-5182 -
obs--98.31 %
Refinement TLS params.

S21: 0.0159 Å ° / 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 °)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)
10.28220.01640.17280.3045-0.00480.2343-0.0025-0.00460.03290-0.0054-0.00360.02780.0025-0.01270.00160.004-0.0174-0.007-0.019547.700216.037724.2138
20.47410.03380.05830.25610.15070.27790.00730.019-0.04030.00890.01920.0185-0.0158-0.0162-0.02120.0015-0.0017-0.0167-0.0006-0.022126.3883-6.452611.0263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 212
2X-RAY DIFFRACTION2B-5 - 212

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