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- PDB-1t5h: 4-Chlorobenzoyl-CoA Ligase/Synthetase unliganded, selenomethionine -

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Basic information

Entry
Database: PDB / ID: 1t5h
Title4-Chlorobenzoyl-CoA Ligase/Synthetase unliganded, selenomethionine
Components4-chlorobenzoyl CoA ligase
KeywordsLIGASE / Adenylate-forming coenzyme A Ligase domain alternation conformational change
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-chlorobenzoyl CoA ligase
Similarity search - Component
Biological speciesAlcaligenes sp. AL3007 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.002 Å
AuthorsGulick, A.M. / Lu, X. / Dunaway-Mariano, D.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structure of 4-Chlorobenzoate:CoA Ligase/Synthetase in the Unliganded and Aryl Substrate-Bound States
Authors: Gulick, A.M. / Lu, X. / Dunaway-Mariano, D.
History
DepositionMay 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: 4-chlorobenzoyl CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8902
Polymers54,8501
Non-polymers401
Water6,125340
1
X: 4-chlorobenzoyl CoA ligase
hetero molecules

X: 4-chlorobenzoyl CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7804
Polymers109,7002
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Unit cell
Length a, b, c (Å)124.979, 124.979, 69.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11X-1140-

HOH

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Components

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


Mass: 54850.059 Da / Num. of mol.: 1
Mutation: SeMet1, SeMet7, SeMet102, SeMet185, SeMet203, SeMet284, SeMet310, SeMet315, SeMet324, SeMet404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes sp. AL3007 (bacteria) / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8GN86, EC: 6.2.1.33
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.84 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 6-8% PEG 4000; 10% glycerol; 0.25 M CaCl2; 50 mM CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.950038 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.950038 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 41528 / Num. obs: 41528 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.516 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
PHASESphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MAD / Resolution: 2.002→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.794 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20578 2102 5.1 %RANDOM
Rwork0.18314 ---
obs0.18428 39426 98.72 %-
all-39426 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.54 Å20 Å2
2--1.07 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.002→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 1 340 4077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213807
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.965185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595495
X-RAY DIFFRACTIONr_chiral_restr0.070.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022887
X-RAY DIFFRACTIONr_nbd_refined0.1870.21574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2272
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.222
X-RAY DIFFRACTIONr_mcbond_it0.4151.52479
X-RAY DIFFRACTIONr_mcangle_it0.81423970
X-RAY DIFFRACTIONr_scbond_it1.50631328
X-RAY DIFFRACTIONr_scangle_it2.474.51215
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 143
Rwork0.232 2376
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)
10.82310.0047-0.24760.73060.14511.9072-0.0439-0.045-0.16920.03650.00490.06230.2675-0.21440.0390.0979-0.02830.01940.05850.04020.1139-22.249691.308412.0527
24.4025-1.147-1.3183.2810.68692.5628-0.07410.3078-0.0647-0.00480.04070.221-0.0005-0.1210.03340.0959-0.0188-0.00350.04980.02510.0131-11.372977.16939.9173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA1 - 4011 - 401
2X-RAY DIFFRACTION2XA402 - 503402 - 503

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