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- PDB-4fut: Crystal structure of ATP bound MatB from Rhodopseudomonas palustris -

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Basic information

Entry
Database: PDB / ID: 4fut
TitleCrystal structure of ATP bound MatB from Rhodopseudomonas palustris
ComponentsMalonyl CoA synthetase
KeywordsLIGASE / ANL Superfamily / methymalonyl-CoA synthetase / CoA / methylmalonate / malonate
Function / homology
Function and homology information


Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / medium-chain fatty acid-CoA ligase activity / fatty acid metabolic process / ATP binding
Similarity search - Function
ANL, C-terminal domain / ANL, N-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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme ...ANL, C-terminal domain / ANL, N-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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / 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 / Malonyl CoA synthetase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRank, K.C. / Crosby, H.A. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: Appl.Environ.Microbiol. / Year: 2012
Title: Structure-Guided Expansion of the Substrate Range of Methylmalonyl Coenzyme A Synthetase (MatB) of Rhodopseudomonas palustris.
Authors: Crosby, H.A. / Rank, K.C. / Rayment, I. / Escalante-Semerena, J.C.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Malonyl CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3059
Polymers55,2211
Non-polymers1,0848
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.140, 173.140, 47.739
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Malonyl CoA synthetase


Mass: 55221.270 Da / Num. of mol.: 1 / Fragment: MatB / Mutation: K488A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: matB, RPA0221 / Plasmid: pTEV5 / Production host: Escherichia coli (E. coli) / Strain (production host): JE9314
References: UniProt: Q6ND88, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: (Bis-Tris buffer (100 mM, pH 6.5) containing trimethylammonium chloride (25 mM), polyethylene glycol 8000 (19.5 %, w/v), glycerol (5 %, 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-BM / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 10, 2011
Details: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: bending magnet / 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: 686070 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 47.867
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 7.3 / Num. unique all: 5358 / Rsym value: 0.442 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-rpMatb

Resolution: 2→24.991 Å / SU ML: 0.24 / σ(F): 0.16 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 2718 5.08 %RANDOM
Rwork0.1578 ---
obs0.1598 53454 95.9 %-
all-108020 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.062 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9856 Å2-0 Å20 Å2
2---0.9856 Å2-0 Å2
3---1.9713 Å2
Refinement stepCycle: LAST / Resolution: 2→24.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 68 609 4564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074076
X-RAY DIFFRACTIONf_angle_d1.0525553
X-RAY DIFFRACTIONf_dihedral_angle_d16.3251500
X-RAY DIFFRACTIONf_chiral_restr0.066623
X-RAY DIFFRACTIONf_plane_restr0.004704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9998-2.07130.23612770.16654763X-RAY DIFFRACTION92
2.0713-2.15410.20682380.1514971X-RAY DIFFRACTION94
2.1541-2.25210.20392940.14884913X-RAY DIFFRACTION94
2.2521-2.37080.21582550.15465015X-RAY DIFFRACTION95
2.3708-2.51920.19072560.15015023X-RAY DIFFRACTION95
2.5192-2.71350.18222820.15415048X-RAY DIFFRACTION96
2.7135-2.98610.21362700.16255125X-RAY DIFFRACTION97
2.9861-3.41730.19052710.16365212X-RAY DIFFRACTION98
3.4173-4.30190.18243060.14275241X-RAY DIFFRACTION99
4.3019-24.99250.17762690.15665425X-RAY DIFFRACTION99
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)
10.72290.2360.05750.7053-0.11420.46180.0211-0.0517-0.0167-0.0662-0.005-0.02810.12980.1099-0.01470.20310.0907-0.06130.1587-0.04240.140230.5047-39.9513-2.7242
20.5264-0.1278-0.20.2060.00410.6973-0.0301-0.1174-0.1075-0.0512-0.12760.05670.49860.08350.12590.53210.24070.00440.2125-0.02950.199636.0596-70.74670.8779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:399 )A1 - 399
2X-RAY DIFFRACTION2( CHAIN A AND RESID 400:503 )A400 - 503

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