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- PDB-4wkg: The crystal structure of apo ArnA features an unexpected central ... -

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Basic information

Entry
Database: PDB / ID: 4wkg
TitleThe crystal structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic coop-erativity
ComponentsBifunctional polymyxin resistance protein ArnA
KeywordsTRANSFERASE / ArnA / multi-drug resistance / MDR / polymyxin / dehydrogenase / transformylase / cooperativity / allosteric regulation
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
Rossmann fold - #12230 / 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 / NAD-dependent epimerase/dehydratase ...Rossmann fold - #12230 / 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 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Bifunctional polymyxin resistance protein ArnA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGrimm, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic cooperativity.
Authors: Fischer, U. / Hertlein, S. / Grimm, C.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional polymyxin resistance protein ArnA
B: Bifunctional polymyxin resistance protein ArnA
C: Bifunctional polymyxin resistance protein ArnA
D: Bifunctional polymyxin resistance protein ArnA
E: Bifunctional polymyxin resistance protein ArnA
F: Bifunctional polymyxin resistance protein ArnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,74110
Polymers446,3156
Non-polymers4274
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25100 Å2
ΔGint-122 kcal/mol
Surface area152420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.720, 112.820, 113.610
Angle α, β, γ (deg.)81.92, 82.96, 83.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bifunctional polymyxin resistance protein ArnA / Polymyxin resistance protein PmrI


Mass: 74385.773 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12
References: UniProt: P77398, UDP-4-amino-4-deoxy-L-arabinose formyltransferase, UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating)
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG8000, 0.2M Magnesium Acetate, 0.1M MOPS pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97661 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97661 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 138756 / Num. obs: 138756 / % possible obs: 97.45 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.04712 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.2 / Num. unique all: 13948 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1z7e

1z7e


Resolution: 2.7→48.157 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 6967 5.02 %
Rwork0.2054 --
obs0.2067 138739 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30190 0 24 9 30223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00530956
X-RAY DIFFRACTIONf_angle_d1.06442062
X-RAY DIFFRACTIONf_dihedral_angle_d13.57211236
X-RAY DIFFRACTIONf_chiral_restr0.0444665
X-RAY DIFFRACTIONf_plane_restr0.0055471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73060.39292260.36694362X-RAY DIFFRACTION97
2.7306-2.76280.3692360.36564407X-RAY DIFFRACTION97
2.7628-2.79640.38072220.34414371X-RAY DIFFRACTION97
2.7964-2.83180.36482480.33634310X-RAY DIFFRACTION97
2.8318-2.86910.38652520.32634359X-RAY DIFFRACTION97
2.8691-2.90840.36982190.31364431X-RAY DIFFRACTION97
2.9084-2.94990.33722410.314343X-RAY DIFFRACTION97
2.9499-2.9940.32872140.2994441X-RAY DIFFRACTION98
2.994-3.04070.34522380.29884430X-RAY DIFFRACTION98
3.0407-3.09060.30482220.28914358X-RAY DIFFRACTION98
3.0906-3.14390.3012510.28774465X-RAY DIFFRACTION98
3.1439-3.2010.32112330.28564319X-RAY DIFFRACTION97
3.201-3.26260.2932400.26924430X-RAY DIFFRACTION98
3.2626-3.32920.29062390.254442X-RAY DIFFRACTION98
3.3292-3.40150.28692270.2484416X-RAY DIFFRACTION98
3.4015-3.48060.28522380.23854376X-RAY DIFFRACTION98
3.4806-3.56770.27422290.22744402X-RAY DIFFRACTION97
3.5677-3.66410.24532330.21884386X-RAY DIFFRACTION97
3.6641-3.77190.24372290.21284404X-RAY DIFFRACTION98
3.7719-3.89360.23322440.20364420X-RAY DIFFRACTION98
3.8936-4.03270.23132430.20024403X-RAY DIFFRACTION98
4.0327-4.1940.2252500.18664414X-RAY DIFFRACTION98
4.194-4.38480.18492480.16854342X-RAY DIFFRACTION98
4.3848-4.61580.182050.16424413X-RAY DIFFRACTION97
4.6158-4.90470.19172300.15734411X-RAY DIFFRACTION98
4.9047-5.2830.19782080.16594418X-RAY DIFFRACTION98
5.283-5.81380.222300.18494411X-RAY DIFFRACTION98
5.8138-6.65320.20672370.1964410X-RAY DIFFRACTION97
6.6532-8.37520.19662130.17234318X-RAY DIFFRACTION96
8.3752-48.16480.15992220.15724360X-RAY DIFFRACTION96
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)
13.3538-0.52410.50031.30030.33461.82470.0862-0.41540.45980.1623-0.0017-0.1978-0.533-0.1146-0.06650.7617-0.10040.12240.314-0.09150.376311.994910.8729104.9911
20.6682-0.0409-0.12421.4254-0.27650.2979-0.0196-0.17350.32310.41610.0284-0.0536-0.4532-0.01970.00450.6432-0.009-0.00670.2257-0.07220.360720.878144.345775.1708
31.61960.3880.11590.83410.17940.876-0.2116-0.6122-0.34740.31290.1173-0.20310.57670.7538-0.09970.29620.4665-0.09431.46570.08350.393877.85981.939825.6725
40.57710.3249-0.36460.6488-0.24671.4237-0.0106-0.0881-0.07910.3277-0.0866-0.3076-0.00530.56810.11150.2729-0.0311-0.08730.5185-0.03820.371454.643715.565260.694
51.28140.31030.01991.21110.16567.4154-0.0282-0.0403-0.11520.12080.20660.00890.26990.5704-0.19140.46750.1438-0.05490.36450.06010.430910.466583.814329.5126
61.5165-0.5923-0.34230.34630.47741.29050.06510.28560.4445-0.02970.0907-0.1776-0.52280.2645-0.1730.5009-0.13520.03240.36890.1360.525644.14752.619333.7104
72.22960.40030.29531.4372-0.26242.7432-0.1621-0.4009-0.06470.1684-0.1291.12960.7024-1.73050.28030.68-0.18660.10981.14960.02431.1829-19.627670.049742.2368
80.68020.42430.40571.6042-0.02651.57810.04070.0476-0.00290.15680.08210.3299-0.1028-0.6459-0.15720.2010.08310.02620.47860.01730.3667-6.579724.703553.1608
92.5109-0.2086-0.02191.13180.03931.10.10180.1831-0.502-0.05190.0181-0.21430.38920.0264-0.11970.7437-0.0522-0.03110.2242-0.05190.469420.1844-18.751187.9063
101.0499-0.3472-0.03180.67370.11241.7835-0.04320.2304-0.4468-0.0323-0.00790.06630.55340.04190.07020.4002-0.04580.030.2271-0.0840.36326.5179-7.545943.7211
111.60690.9220.05241.90850.04031.2699-0.50280.24260.1985-0.67040.30250.22620.02950.33950.17570.57680.0013-0.17310.7283-0.03670.337160.548711.4034-3.854
120.9731-0.26350.07542.1006-0.19760.48650.0040.51920.0943-0.73060.04140.40150.011-0.1058-0.02830.6068-0.083-0.0920.75590.06770.346218.405129.481513.4899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 281 )
2X-RAY DIFFRACTION2chain 'A' and (resid 282 through 656 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 281 )
4X-RAY DIFFRACTION4chain 'B' and (resid 282 through 656 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 281 )
6X-RAY DIFFRACTION6chain 'C' and (resid 282 through 656 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 281 )
8X-RAY DIFFRACTION8chain 'D' and (resid 282 through 655 )
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 281 )
10X-RAY DIFFRACTION10chain 'E' and (resid 282 through 656 )
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 281 )
12X-RAY DIFFRACTION12chain 'F' and (resid 282 through 656 )

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