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- PDB-4b4u: Crystal structure of Acinetobacter baumannii N5, N10- methylenete... -

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Basic information

Entry
Database: PDB / ID: 4b4u
TitleCrystal structure of Acinetobacter baumannii N5, N10- methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD) complexed with NADP cofactor
ComponentsBIFUNCTIONAL PROTEIN FOLD
KeywordsOXIDOREDUCTASE
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 / nucleotide binding / cytosol
Similarity search - Function
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 ...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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / Bifunctional protein FolD
Similarity search - Component
Biological speciesACINETOBACTER BAUMANNII ATCC 19606 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsEadsforth, T.C. / Maluf, F.V. / Hunter, W.N.
CitationJournal: FEBS J. / Year: 2012
Title: Acinetobacter Baumannii Fold Ligand Complexes; Potent Inhibitors of Folate Metabolism and a Re-Evaluation of the Ly374571 Structure.
Authors: Eadsforth, T.C. / Maluf, F.V. / Hunter, W.N.
History
DepositionAug 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3Dec 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,37315
Polymers64,2922
Non-polymers2,08113
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-39.9 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.036, 80.126, 68.620
Angle α, β, γ (deg.)90.00, 107.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32146.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER BAUMANNII ATCC 19606 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D0CBC8, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase

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Non-polymers , 5 types, 753 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.4 Å3/Da / Density % sol: 49.2 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS PH 5.5, 25 % PEG 3350, 0.2M MGCL AND 2 % DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.981
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 1.45→52.6 Å / Num. obs: 100394 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B0A

1b0a


Resolution: 1.45→52.6 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.738 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES WITH DISORDERED SIDE CHAINS ARE MODELED WITH AN OCCUPANCY OF 0.00. DISORDERED NICOTINAMIDE AND RIBOSE.
RfactorNum. reflection% reflectionSelection details
Rfree0.15151 5019 5 %RANDOM
Rwork0.12173 ---
obs0.12319 95345 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.28 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.45→52.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 94 740 5020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194470
X-RAY DIFFRACTIONr_bond_other_d0.0010.022991
X-RAY DIFFRACTIONr_angle_refined_deg1.4782.0046097
X-RAY DIFFRACTIONr_angle_other_deg0.94837409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4425621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12425.329167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87715796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.381526
X-RAY DIFFRACTIONr_chiral_restr0.0820.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02779
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.04737461
X-RAY DIFFRACTIONr_sphericity_free27.9335179
X-RAY DIFFRACTIONr_sphericity_bonded8.8857951
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 350 -
Rwork0.197 6893 -
obs--98.49 %

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