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- PDB-4a5o: Crystal structure of Pseudomonas aeruginosa N5, N10- methylenetet... -

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Basic information

Entry
Database: PDB / ID: 4a5o
TitleCrystal structure of Pseudomonas aeruginosa N5, N10- methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD)
ComponentsBIFUNCTIONAL PROTEIN FOLD
KeywordsOXIDOREDUCTASE / HYDROLASE
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 / one-carbon metabolic process / cytosol
Similarity search - Function
Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Bifunctional protein FolD
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEadsforth, T.C. / Gardiner, M. / Maluf, F.V. / McElroy, S. / James, D. / Frearson, J. / Gray, D. / Hunter, W.N.
CitationJournal: Plos One / Year: 2012
Title: Assessment of Pseudomonas Aeruginosa N(5),N(10)-Methylenetetrahydrofolate Dehydrogenase - Cyclohydrolase as a Potential Antibacterial Drug Target.
Authors: Eadsforth, T.C. / Gardiner, M. / Maluf, F.V. / Mcelroy, S. / James, D. / Frearson, J. / Gray, D. / Hunter, W.N.
History
DepositionOct 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
C: BIFUNCTIONAL PROTEIN FOLD
D: BIFUNCTIONAL PROTEIN FOLD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3206
Polymers123,1214
Non-polymers1982
Water2,432135
1
A: BIFUNCTIONAL PROTEIN FOLD
B: BIFUNCTIONAL PROTEIN FOLD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7594
Polymers61,5612
Non-polymers1982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-6.2 kcal/mol
Surface area22890 Å2
MethodPISA
2
C: BIFUNCTIONAL PROTEIN FOLD
D: BIFUNCTIONAL PROTEIN FOLD


Theoretical massNumber of molelcules
Total (without water)61,5612
Polymers61,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-7.5 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.570, 82.430, 109.070
Angle α, β, γ (deg.)90.00, 94.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BIFUNCTIONAL PROTEIN FOLD / N5\ / N10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE-CYCLOHYDROLASE / METHYLENETETRAHYDROFOLATE ...N5\ / N10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE-CYCLOHYDROLASE / METHYLENETETRAHYDROFOLATE DEHYDROGENASE / METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE


Mass: 30780.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Plasmid: PA_FOLD_PET15BTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9I2U6, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.46 Å3/Da / Density % sol: 50.06 % / Description: NONE
Crystal growDetails: 25 % PEG 3350, 0.2 M MAGNESIUM FORMATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9814
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 55263 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 41.56 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B0A

1b0a


Resolution: 2.2→39.13 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 17.692 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY DISORDERED SIDE CHAINS ARE MODELLED WITH AN OCCUPANCY OF ZERO
RfactorNum. reflection% reflectionSelection details
Rfree0.27872 2804 5.1 %RANDOM
Rwork0.2338 ---
obs0.23605 52441 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.623 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å2-0 Å2-1.15 Å2
2--0.6 Å2-0 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8454 0 13 135 8602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0218387
X-RAY DIFFRACTIONr_bond_other_d0.0010.025537
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.97811436
X-RAY DIFFRACTIONr_angle_other_deg0.823313489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46351128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28523.958331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.129151301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.211563
X-RAY DIFFRACTIONr_chiral_restr0.0580.21348
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021551
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3661.55565
X-RAY DIFFRACTIONr_mcbond_other0.0611.52282
X-RAY DIFFRACTIONr_mcangle_it0.67728880
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96432822
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5834.52551
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 213 -
Rwork0.301 3801 -
obs--100 %
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)
14.0064-0.75360.82361.7659-0.41312.1364-0.18170.84150.0625-0.1872-0.1069-0.3585-0.3110.94710.28850.2277-0.1767-0.00040.6190.15620.238416.539317.040929.9578
22.9920.06770.3141.7298-0.9922.8773-0.03020.2534-0.1357-0.08980.02230.1165-0.03550.28380.00790.1314-0.0038-0.02520.05510.00670.1343-2.252610.197135.0084
34.08030.82780.88992.78920.11441.9741-0.0261-0.260.12220.40380.1178-0.26350.30320.5758-0.09170.26580.2285-0.05580.3981-0.0420.204215.5465-15.738555.358
44.6408-1.49411.40573.622-1.4832.5151-0.0383-0.0867-0.00120.14270.2280.47950.1630.184-0.18970.19240.08370.01360.06720.01030.1451-2.4031-9.774248.1399
55.2429-2.16760.00562.88150.75657.7018-0.05920.39760.1845-0.85840.6297-0.4328-2.08052.7706-0.57061.0569-0.92880.24871.377-0.32250.360822.937516.5105-25.255
62.66310.33730.74341.56310.54088.3813-0.1106-0.01290.0276-0.15160.26920.1052-1.17220.3857-0.15860.3988-0.01730.02180.1440.02080.13733.270510.3543-21.8648
72.23131.42840.74014.41840.32612.8799-0.0452-0.2778-0.47860.8490.4075-0.75270.95161.127-0.36230.65110.5503-0.13030.8973-0.11310.440820.2018-12.2586-2.598
86.123-1.72121.41914.6519-0.94658.3433-0.0616-0.67950.05040.66610.2460.04831.0168-0.2485-0.18440.47280.06590.06550.19280.03570.1353-1.0361-10.4333-8.566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 111
2X-RAY DIFFRACTION2A112 - 284
3X-RAY DIFFRACTION3B1 - 111
4X-RAY DIFFRACTION4B112 - 284
5X-RAY DIFFRACTION5C2 - 113
6X-RAY DIFFRACTION6C114 - 284
7X-RAY DIFFRACTION7D2 - 139
8X-RAY DIFFRACTION8D140 - 282

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