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- PDB-2qvy: 4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3... -

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Basic information

Entry
Database: PDB / ID: 2qvy
Title4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate
Components4-Chlorobenzoate CoA Ligase
KeywordsLIGASE / Adenylate-forming enzymes / Acyl-CoA ligase
Function / homology
Function and homology information


medium-chain fatty acid-CoA ligase activity / fatty acid metabolic process / nucleotide binding / membrane / metal ion binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3,4-dichlorobenzoate / 4-chlorobenzoyl CoA ligase
Similarity search - Component
Biological speciesAlcaligenes sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsWu, R. / Reger, A.S. / Cao, J. / Gulick, A.M. / Dunaway-Mariano, D.
CitationJournal: Biochemistry / Year: 2007
Title: Rational redesign of the 4-chlorobenzoate binding site of 4-chlorobenzoate: coenzyme a ligase for expanded substrate range.
Authors: Wu, R. / Reger, A.S. / Cao, J. / Gulick, A.M. / Dunaway-Mariano, D.
History
DepositionAug 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE AUTHOR MENTIONED THAT THE SEQUENCE USED IN THIS ENTRY MATCHES THE GB ACCESSION CODE ...SEQUENCE THE AUTHOR MENTIONED THAT THE SEQUENCE USED IN THIS ENTRY MATCHES THE GB ACCESSION CODE AAN10109 AND IS MUTATED AT RESIDUE 303 (I303G).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 4-Chlorobenzoate CoA Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5162
Polymers54,3251
Non-polymers1911
Water45025
1
X: 4-Chlorobenzoate CoA Ligase
hetero molecules

X: 4-Chlorobenzoate CoA Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0324
Polymers108,6502
Non-polymers3822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Unit cell
Length a, b, c (Å)127.813, 127.813, 71.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 4-Chlorobenzoate CoA Ligase


Mass: 54325.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes sp. (bacteria) / Strain: AL3007 / Plasmid: pQE-70 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8GN86*PLUS, EC: 6.2.1.33
#2: Chemical ChemComp-34Z / 3,4-dichlorobenzoate


Mass: 191.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4Cl2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 14-22% pentaerythritol propoxylate 426, 50 mM BTP, 1 mM ATP, 1 mM 3,4-DCB, pH 6.5-6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.76→30 Å / Num. obs: 17323 / % possible obs: 99.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.5
Reflection shellResolution: 2.76→2.83 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5D

1t5d


Resolution: 2.76→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 30.392 / SU ML: 0.283 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.871 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25651 872 5 %RANDOM
Rwork0.19136 ---
obs0.19455 16440 99.87 %-
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: 57.054 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.76→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 11 25 3752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223795
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.975173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3755496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09922.987154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.47215583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7821534
X-RAY DIFFRACTIONr_chiral_restr0.1140.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022886
X-RAY DIFFRACTIONr_nbd_refined0.2420.21803
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22610
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.24
X-RAY DIFFRACTIONr_mcbond_it2.64922525
X-RAY DIFFRACTIONr_mcangle_it4.02833971
X-RAY DIFFRACTIONr_scbond_it3.00321387
X-RAY DIFFRACTIONr_scangle_it4.45731202
LS refinement shellResolution: 2.76→2.833 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 61 -
Rwork0.295 1007 -
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)
14.04252.3112-2.29162.3403-1.89232.7304-0.08550.78410.13990.23780.26210.3079-0.002-0.6894-0.1765-0.244-0.04350.12610.0199-0.0089-0.11397.6533-46.6318-10.7108
23.43171.6118-0.27354.3829-1.3745.54830.5974-0.29770.14820.6004-0.30530.2051-0.62380.4368-0.29210.047-0.11680.1929-0.02860.0159-0.1394-0.0397-62.025116.7429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA1 - 4021 - 402
2X-RAY DIFFRACTION2XA403 - 502403 - 502

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