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- PDB-4gxr: Structure of ATP bound RpMatB-BxBclM chimera B3 -

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Basic information

Entry
Database: PDB / ID: 4gxr
TitleStructure of ATP bound RpMatB-BxBclM chimera B3
ComponentsMalonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein
KeywordsLIGASE / RpMatB-BxBclM chimera / ANL-superfamily / methylmalonate-CoA ligase / malonate-CoA ligase / CoA / methylmalonate / malonate / acetylation of K488 by RpPat
Function / homology
Function and homology information


3-(methylthio)propionyl-CoA ligase / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty acid-CoA ligase activity / secondary metabolite biosynthetic process / fatty acid metabolic process / ATP binding / membrane
Similarity search - Function
Benzoate-CoA ligase family / ANL, N-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme ...Benzoate-CoA ligase family / ANL, N-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CARBONATE ION / Benzoate-CoA ligase / 3-methylmercaptopropionyl-CoA ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
Burkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRank, K.C. / Crosby, H.A. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Insights into the Substrate Specificity of the Rhodopseudomonas palustris Protein Acetyltransferase RpPat: IDENTIFICATION OF A LOOP CRITICAL FOR RECOGNITION BY RpPat.
Authors: Crosby, H.A. / Rank, K.C. / Rayment, I. / Escalante-Semerena, J.C.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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: Malonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3979
Polymers55,3411
Non-polymers1,0568
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.155, 173.155, 47.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Malonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein


Mass: 55341.465 Da / Num. of mol.: 1
Fragment: UNP Q6ND88 residues 1-443,455-503 and UNP Q13WK3 473-483
Mutation: K488A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic), (gene. exp.) Burkholderia xenovorans (bacteria)
Strain: CGA009 / Gene: matB, RPA0221 / Plasmid: PTEV5 / Production host: Escherichia coli (E. coli) / Strain (production host): JE9314
References: UniProt: Q6ND88, UniProt: Q13WK3, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases

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Non-polymers , 6 types, 541 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: triethanolamine (100 mM, pH 8.0), with magnesium sulfate (50 mM), monomethyl polyethylene glycol 5000 (21 %, w/v), and glycerol (4 %, w/v), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: ROSENBAUM-ROCK HIGH-RESOLUTION DOUBLE-CRYSTAL MONOCHROMATOR. LN2 COOLED FIRST CRYSTAL, SAGITTAL FOCUSING 2ND CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 345188 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.061 / Rsym value: 0.061
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 6.086 / Num. unique all: 2756 / Rsym value: 0.048 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FUT

4fut


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.081 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17787 2833 5.1 %RANDOM
Rwork0.14833 ---
all0.14982 52933 --
obs0.14982 52933 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.829 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.07 Å20 Å2
2---0.07 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 0 65 533 4495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194109
X-RAY DIFFRACTIONr_bond_other_d0.0010.023985
X-RAY DIFFRACTIONr_angle_refined_deg1.1692.0255597
X-RAY DIFFRACTIONr_angle_other_deg0.69739152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2185521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44923.077169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95715554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7271532
X-RAY DIFFRACTIONr_chiral_restr0.0630.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02900
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 203 -
Rwork0.17 3782 -
obs--98.76 %
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)
10.43440.14020.12310.72010.02570.22010.05640.01320.0287-0.0205-0.0354-0.00070.0102-0.0604-0.02090.07420.0012-0.01310.12220.06680.0807-49.98085.84182.5156
22.3807-0.59950.05561.97590.07441.81840.0099-0.0391-0.1928-0.0434-0.08060.19560.1094-0.32940.07060.0293-0.0543-0.01710.2295-0.0090.1004-79.101-4.4448-1.7336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 400
2X-RAY DIFFRACTION2A401 - 503

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