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- PDB-3p2o: Crystal Structure of FolD Bifunctional Protein from Campylobacter... -

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Basic information

Entry
Database: PDB / ID: 3p2o
TitleCrystal Structure of FolD Bifunctional Protein from Campylobacter jejuni
ComponentsBifunctional protein folD
KeywordsOXIDOREDUCTASE / HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-alpha sandwich / cytosol
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine biosynthetic process / L-histidine biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion / cytosol
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 / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily ...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 / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Bifunctional protein FolD
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.227 Å
AuthorsKim, Y. / Zhang, R. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of FolD Bifunctional Protein from
Authors: Kim, Y. / Zhang, R. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Bifunctional protein folD
B: Bifunctional protein folD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3895
Polymers61,9702
Non-polymers1,4193
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-23 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.927, 44.981, 117.021
Angle α, β, γ (deg.)90.00, 119.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bifunctional protein folD / Methylenetetrahydrofolate dehydrogenase / Methenyltetrahydrofolate cyclohydrolase


Mass: 30984.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj0855, folD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q0PA35, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH5.5, 25 % w/v Polyehtlyene glycol 3350, 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: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 39430 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 62.8 % / Biso Wilson estimate: 44.8 Å2 / Rsym value: 0.042 / Net I/σ(I): 12.4
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.24 / Num. unique all: 1118 / Rsym value: 0.452 / % possible all: 75

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The crystal structure of the same protein in the absence of NAD

Resolution: 2.227→33.593 Å / SU ML: 0.36 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1490 5.07 %random
Rwork0.189 ---
all0.193 29365 --
obs0.1927 29365 97 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.277 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 62.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.8917 Å20 Å20.5809 Å2
2--22.5391 Å20 Å2
3----18.6474 Å2
Refinement stepCycle: LAST / Resolution: 2.227→33.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4250 0 94 105 4449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014428
X-RAY DIFFRACTIONf_angle_d1.2496007
X-RAY DIFFRACTIONf_dihedral_angle_d19.7251756
X-RAY DIFFRACTIONf_chiral_restr0.074739
X-RAY DIFFRACTIONf_plane_restr0.006747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2268-2.30640.34241150.262190230578
2.3064-2.39870.33581390.25852692283194
2.3987-2.50780.35121510.249328673018100
2.5078-2.640.31581240.229728682992100
2.64-2.80530.3321760.228428162992100
2.8053-3.02180.30381440.219928482992100
3.0218-3.32570.28531590.225928593018100
3.3257-3.80630.23851580.202929033061100
3.8063-4.79330.21231420.150929053047100
4.7933-33.59690.21641820.15162927310999
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)
11.7963-0.02450.30930.61650.03571.6554-0.0783-0.0137-0.11960.1354-0.121-0.0286-0.0126-0.09630.13540.3054-0.03380.02460.2213-0.04840.284422.7328-22.9-24.3181
22.28790.6052-0.47390.861-0.63071.6351-0.0974-0.1344-0.26050.0948-0.3128-0.287-0.17640.9480.35180.303-0.0597-0.03830.59550.19840.43754.8644-25.1214-27.9546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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