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- PDB-6de8: Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydro... -

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Basic information

Entry
Database: PDB / ID: 6de8
TitleCrystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase from Campylobacter jejuni
ComponentsBifunctional protein FolD
KeywordsOXIDOREDUCTASE / MTHFDC / alpha-beta-fold / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine biosynthetic process / histidine biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion
Similarity search - Function
Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
IODIDE ION / : / Bifunctional protein FolD
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.104 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Zhang, R. / Peterson, S.N. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase from Campylobacter jejuni
Authors: Kim, Y. / Makowska-Grzyska, M. / Zhang, R. / Peterson, S.N. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein FolD
B: Bifunctional protein FolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,38623
Polymers61,9702
Non-polymers2,41621
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-28 kcal/mol
Surface area23490 Å2
2
A: Bifunctional protein FolD
B: Bifunctional protein FolD
hetero molecules

A: Bifunctional protein FolD
B: Bifunctional protein FolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,77246
Polymers123,9404
Non-polymers4,83242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15210 Å2
ΔGint-67 kcal/mol
Surface area45910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.887, 59.253, 73.240
Angle α, β, γ (deg.)90.00, 100.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional protein FolD /


Mass: 30984.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: folD, Cj0855 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 magic
References: UniProt: Q0PA35, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase

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Non-polymers , 5 types, 419 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M potassium iodide, 20 % (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 40403 / % possible obs: 99.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 32.92 Å2 / CC1/2: 0.651 / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.881 / Num. unique obs: 2008 / CC1/2: 0.651 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.104→42.77 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.87
RfactorNum. reflection% reflection
Rfree0.2259 2037 5.04 %
Rwork0.1894 --
obs0.1912 40385 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.104→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 31 398 4665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024296
X-RAY DIFFRACTIONf_angle_d0.4655806
X-RAY DIFFRACTIONf_dihedral_angle_d12.9482656
X-RAY DIFFRACTIONf_chiral_restr0.044718
X-RAY DIFFRACTIONf_plane_restr0.003730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1045-2.15340.29231220.2512413X-RAY DIFFRACTION95
2.1534-2.20730.29781230.24782588X-RAY DIFFRACTION100
2.2073-2.2670.34661570.27892499X-RAY DIFFRACTION100
2.267-2.33370.28431160.2372563X-RAY DIFFRACTION100
2.3337-2.4090.24961360.21542560X-RAY DIFFRACTION100
2.409-2.49510.27951150.20812567X-RAY DIFFRACTION100
2.4951-2.5950.24791410.20452544X-RAY DIFFRACTION100
2.595-2.7130.23721320.21212585X-RAY DIFFRACTION100
2.713-2.8560.25691450.21022538X-RAY DIFFRACTION100
2.856-3.03490.26551370.20082575X-RAY DIFFRACTION100
3.0349-3.26920.23841560.1972543X-RAY DIFFRACTION100
3.2692-3.5980.20871270.18252582X-RAY DIFFRACTION100
3.598-4.11830.191270.15872595X-RAY DIFFRACTION100
4.1183-5.18720.17261430.14732585X-RAY DIFFRACTION100
5.1872-42.7790.19631600.17222611X-RAY DIFFRACTION99
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)
13.47123.40540.0233.40931.17961.32520.3333-0.460.16070.3263-0.32460.2414-0.0559-0.2567-0.03330.23690.00980.02890.3519-0.05010.31726.9269-2.654828.1347
23.3817-0.7055-0.15491.56270.22811.79210.0605-0.20580.00050.1053-0.0065-0.0114-0.00070.0816-0.06240.259-0.0176-0.01280.20960.01330.204524.6337-16.418522.6719
30.6315-0.641-1.22481.69751.30482.04120.1014-0.11250.1292-0.0059-0.06470.0423-0.2367-0.08810.13160.27810.01910.00520.2448-0.00120.261915.7786-1.945612.2179
41.80410.2344-0.61111.0595-0.0592.6850.2076-0.17550.31630.1288-0.07560.0288-0.3690.0853-0.120.2891-0.04150.05440.2091-0.02480.251324.587612.86319.0749
53.53523.55021.17457.23312.29843.21360.14030.0417-0.064-0.3918-0.18280.2825-0.2159-0.27260.16620.21890.0543-0.01520.33670.00740.254312.0805-8.254121.3574
61.0868-1.3776-1.00812.18311.05460.76440.07120.09750.0289-0.2692-0.0262-0.2067-0.0830.1087-0.09140.2452-0.002-0.00590.35380.02330.219539.74-3.2072-19.777
75.16290.3527-0.46211.8272-0.23793.37950.00980.30680.2791-0.118-0.02350.2563-0.0692-0.2515-0.01340.20080.0149-0.03870.2025-0.01110.25118.4051-11.6215-16.115
81.51291.7543-1.70542.3406-1.85711.58510.1819-0.0772-0.1790.139-0.2106-0.0558-0.18640.06160.13710.2297-0.0262-0.0120.2633-0.0030.270431.5477-1.9664-3.9464
92.2733-0.0145-1.55631.9122-0.58992.67050.16910.33780.3452-0.09890.05050.1614-0.3126-0.2683-0.17950.30480.03040.00940.27410.02730.287427.09715.0808-7.1402
104.4414-2.42580.31712.0676-1.53014.4847-0.0826-0.2442-0.30830.20140.0739-0.0471-0.09670.2358-0.01140.2153-0.00980.01940.38460.00180.246932.7689-7.9914-13.6067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 260 )
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 281 )
6X-RAY DIFFRACTION6chain 'B' and (resid -1 through 26 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 120 )
8X-RAY DIFFRACTION8chain 'B' and (resid 121 through 150 )
9X-RAY DIFFRACTION9chain 'B' and (resid 151 through 260 )
10X-RAY DIFFRACTION10chain 'B' and (resid 261 through 281 )

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