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- PDB-4b4w: Crystal structure of Acinetobacter baumannii N5, N10- methylenete... -

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Basic information

Entry
Database: PDB / ID: 4b4w
TitleCrystal structure of Acinetobacter baumannii N5, N10- methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD) complexed with NADP cofactor and an inhibitor
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
Chem-9L9 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Bifunctional protein FolD
Similarity search - Component
Biological speciesACINETOBACTER BAUMANNII ATCC 19606 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)66,8659
Polymers64,2922
Non-polymers2,5737
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-16.9 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.541, 80.882, 68.482
Angle α, β, γ (deg.)90.00, 106.60, 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, 599 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-9L9 / (2S)-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]pentanedioic acid


Mass: 433.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N7O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.44 Å3/Da / Density % sol: 49.5 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS PH 5.5, 20 % PEG 3350, 0.2 M MGCL2 AND 2 % DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20.86 Å / Num. obs: 38850 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 8.1 / % possible all: 99.1

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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: 2→20.86 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.225 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED NICOTINAMIDE AND RIBOSE. RESIDUES WITH DISORDERED SIDE CHAINS ARE MODELED WITH AN OCCUPANCY OF 0.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.21346 1940 5 %RANDOM
Rwork0.17052 ---
obs0.17269 36878 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20.93 Å2
2---0.46 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2→20.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 137 592 4881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194336
X-RAY DIFFRACTIONr_bond_other_d0.0010.022836
X-RAY DIFFRACTIONr_angle_refined_deg1.1482.0175900
X-RAY DIFFRACTIONr_angle_other_deg0.8543.0026973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1115572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86825.263152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27815736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9431524
X-RAY DIFFRACTIONr_chiral_restr0.0570.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02743
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 113 -
Rwork0.209 2624 -
obs--98.14 %
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)
11.1976-0.1985-0.79981.43470.16812.27470.0369-0.0048-0.0223-0.2733-0.0137-0.1415-0.11510.0634-0.02320.0823-0.01760.01580.031-0.00730.036318.23040.888429.6528
23.1416-0.0212-0.99221.16230.10251.5374-0.07190.3796-0.3032-0.1619-0.11590.20460.0626-0.37780.18780.09840.0027-0.02260.1283-0.07410.08310.8114-0.971726.2256
30.59260.3177-0.21251.6136-0.26681.81140.0836-0.07140.03650.2628-0.05660.0805-0.24960.0215-0.0270.0742-0.00970.00490.0098-0.00810.025311.26845.250364.9583
41.6839-0.00360.96090.8665-0.02132.3198-0.0950.0114-0.06720.1375-0.04570.28820.024-0.40190.14070.032-0.02690.05410.0972-0.05760.1309-6.19320.790854.4831
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 175
2X-RAY DIFFRACTION2A176 - 282
3X-RAY DIFFRACTION3B1 - 133
4X-RAY DIFFRACTION4B134 - 282

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