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- PDB-3cw9: 4-Chlorobenzoyl-CoA Ligase/Synthetase in the Thioester-forming Co... -

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Basic information

Entry
Database: PDB / ID: 3cw9
Title4-Chlorobenzoyl-CoA Ligase/Synthetase in the Thioester-forming Conformation, bound to 4-chlorophenacyl-CoA
Components4-chlorobenzoyl CoA ligase
KeywordsLIGASE / Adenylate-forming enzymes / Acyl-CoA ligase / Domain Alternation
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, C-terminal domain superfamily / AMP-binding enzyme / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
4-Chlorophenacyl-coenzyme A / ADENOSINE MONOPHOSPHATE / NITRATE ION / 4-chlorobenzoyl CoA ligase
Similarity search - Component
Biological speciesAlcaligenes sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReger, A.S. / Cao, J. / Wu, R. / Dunaway-Mariano, D. / Gulick, A.M.
Citation
Journal: Biochemistry / Year: 2008
Title: Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase.
Authors: Reger, A.S. / Wu, R. / Dunaway-Mariano, D. / Gulick, A.M.
#1: Journal: To be Published / Year: 2008
Title: Mechanism of 4-Chlorobenzoate: Coenzyme A Ligase Catalysis
Authors: Wu, R. / Cao, J. / Lu, X. / Reger, A.S. / Gulick, A.M. / Dunaway-Mariano, D.
History
DepositionApr 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: 4-chlorobenzoyl CoA ligase
B: 4-chlorobenzoyl CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,59412
Polymers108,7622
Non-polymers2,83110
Water14,412800
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-9.8 kcal/mol
Surface area37710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.507, 87.789, 186.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4-chlorobenzoyl CoA ligase / E.C.6.2.1.33 / Chlorobenzoate CoA Ligase/Synthetase


Mass: 54381.109 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 810 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-01A / 4-Chlorophenacyl-coenzyme A


Mass: 920.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H41ClN7O17P3S
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 800 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE IN THIS ENTRY CORRESPONDS TO THE SEQUENCE FROM GB ENTRY AAN10109.

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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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14-18% PEG 1000, 75 mM Magnesium Nitrate, 100 mM MOPS, 1 mM AMP, 1 mM 4-Chlorophenacyl-CoA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979469 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2006
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979469 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 64355 / Num. obs: 60959 / % possible obs: 94.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 30.9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 6.7 / Num. unique all: 3442 / % possible all: 74.3

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Processing

Software
NameVersionClassification
SSRLremote data collection interfacedata collection
MOLREPphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5D, residues 1-402

1t5d


Resolution: 2→35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.866 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20912 3258 5.1 %RANDOM
Rwork0.16576 ---
all0.16798 64355 --
obs0.16798 60959 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.886 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2---1.54 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7604 0 180 800 8584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227932
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.99110819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6451004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57123.07329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.126151235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1111572
X-RAY DIFFRACTIONr_chiral_restr0.0760.21259
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025994
X-RAY DIFFRACTIONr_nbd_refined0.1830.23744
X-RAY DIFFRACTIONr_nbtor_refined0.2970.25422
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2804
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.238
X-RAY DIFFRACTIONr_mcbond_it0.4541.55180
X-RAY DIFFRACTIONr_mcangle_it0.75928054
X-RAY DIFFRACTIONr_scbond_it1.32333104
X-RAY DIFFRACTIONr_scangle_it2.1764.52765
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 174 -
Rwork0.174 3442 -
obs--73.65 %
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)
10.14790.00960.12290.5671-0.05780.3578-0.00570.0370.02790.06040.01250.0334-0.03260.0217-0.0068-0.0188-0.00570.0009-0.02980.0033-0.024522.638417.672468.6896
20.88130.2210.54831.7507-0.46511.4638-0.08710.04620.02320.1286-0.0626-0.1728-0.09810.05690.1497-0.0015-0.0021-0.044-0.05410.0128-0.018438.773538.918480.2665
30.4144-0.0292-0.00870.39910.0380.1199-0.01230.0202-0.01970.01890.010.00320.0015-0.00480.0023-0.0058-0.00310.0022-0.02520.0006-0.037421.792-16.449568.1431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 402
2X-RAY DIFFRACTION2A403 - 503
3X-RAY DIFFRACTION3B1 - 402

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