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- PDB-2bll: Apo-structure of the C-terminal decarboxylase domain of ArnA -

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Basic information

Entry
Database: PDB / ID: 2bll
TitleApo-structure of the C-terminal decarboxylase domain of ArnA
ComponentsPROTEIN YFBG
KeywordsTRANSFERASE / DECARBOXYLASE / SHORT CHAIN DEHYDROGENASE / L-ARA4N BIOSYNTHESIS / METHYLTRANSFERASE
Function / homology
Function and homology information


UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding ...UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding / response to antibiotic / protein-containing complex / identical protein binding
Similarity search - Function
Bifunctional polymyxin resistance protein, ArnA / Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 ...Bifunctional polymyxin resistance protein, ArnA / Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional polymyxin resistance protein ArnA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsWilliams, G.J. / Breazeale, S.D. / Raetz, C.R.H. / Naismith, J.H.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and Function of Both Domains of Arna, a Dual Function Decarboxylase and a Formyltransferase, Involved in 4-Amino-4-Deoxy-L- Arabinose Biosynthesis.
Authors: Williams, G.J. / Breazeale, S.D. / Raetz, C.R.H. / Naismith, J.H.
History
DepositionMar 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN YFBG


Theoretical massNumber of molelcules
Total (without water)40,0581
Polymers40,0581
Non-polymers00
Water1,69394
1
A: PROTEIN YFBG

A: PROTEIN YFBG


Theoretical massNumber of molelcules
Total (without water)80,1152
Polymers80,1152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_545-x+1/4,z-1/4,y+1/41
MethodPQS
Unit cell
Length a, b, c (Å)149.438, 149.438, 149.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein PROTEIN YFBG / UDP-D-GLUCURONATE DEHYDROGENASE ARNA


Mass: 40057.586 Da / Num. of mol.: 1 / Fragment: DECARBOXYLASE DOMAIN, RESIDUES 317-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3310 / Plasmid: PET24B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77398, UDP-glucuronate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL DECARBOXYLASE DOMAIN FROM T316M TO S660

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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: 3.5 Å3/Da / Density % sol: 64.3 %
Crystal growpH: 5.2 / Details: 3.2 M NACL, 0.1 M BIS-TRIS PH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 19, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→87.7 Å / Num. obs: 25160 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 16.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→87.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.846 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A LOOP CONTAINING RESIDUES V604-D615 IS MISSING IN THE STRUCTURE. THE C-TERMINAL RESIDUES K658-S660 ARE MISSING IN THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1275 5.1 %RANDOM
Rwork0.186 ---
obs0.188 23801 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→87.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 0 94 2799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222800
X-RAY DIFFRACTIONr_bond_other_d0.0010.022559
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.953790
X-RAY DIFFRACTIONr_angle_other_deg0.89935933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9423.154149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60315491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9011527
X-RAY DIFFRACTIONr_chiral_restr0.0990.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
X-RAY DIFFRACTIONr_nbd_refined0.20.2593
X-RAY DIFFRACTIONr_nbd_other0.1960.22693
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21356
X-RAY DIFFRACTIONr_nbtor_other0.090.21619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2971.52128
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52722684
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.44931335
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5944.51106
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 88
Rwork0.211 1771
Refinement TLS params.Method: refined / Origin x: 28.69 Å / Origin y: -24.585 Å / Origin z: -10.671 Å
111213212223313233
T-0.057 Å20.035 Å2-0.1054 Å2--0.0916 Å2-0.0347 Å2---0.023 Å2
L0.8973 °2-0.1018 °20.1702 °2-1.3205 °2-0.0495 °2--1.1927 °2
S-0.0905 Å °-0.0074 Å °0.2103 Å °-0.0143 Å °0.0268 Å °-0.1501 Å °-0.2304 Å °0.0365 Å °0.0637 Å °

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