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- PDB-4gxq: Crystal Structure of ATP bound RpMatB-BxBclM chimera B1 -

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Basic information

Entry
Database: PDB / ID: 4gxq
TitleCrystal Structure of ATP bound RpMatB-BxBclM chimera B1
ComponentsMalonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein
KeywordsLIGASE / RpMatB-BxBclM chimera / ANL Superfamily / methylmalonate-CoA ligase / malonate-CoA ligase / methylmalonate / malonate
Function / homology
Function and homology information


benzoate-CoA ligase / benzoate-CoA ligase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / ligase activity / ATP binding / membrane
Similarity search - Function
Benzoate-CoA ligase family / 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 ...Benzoate-CoA ligase family / 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, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CARBONATE ION / Benzoate-CoA ligase / Malonyl CoA synthetase
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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, Benzoate-CoA ligase Chimeric protein
B: Malonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein
C: Malonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,45112
Polymers167,6773
Non-polymers1,7749
Water28,5721586
1
A: Malonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4844
Polymers55,8921
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Malonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4844
Polymers55,8921
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Malonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4844
Polymers55,8921
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)299.305, 299.305, 47.909
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, Benzoate-CoA ligase Chimeric protein


Mass: 55892.242 Da / Num. of mol.: 3
Fragment: UNP Q6ND88 residues 1-443,466-506 and UNP Q13WK3 473-497
Mutation: K491A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic), (gene. exp.) Burkholderia xenovorans (bacteria)
Strain: CGA009, LB400 / 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
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1586 / 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: 3.69 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES buffer (100 mM, pH 7.5), 200 mM potassium glutamate, polyethylene glycol 8000 (26 % (w/v), propylene glycol (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-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: 850800 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.073 / Rsym value: 0.073
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.8 / Num. unique all: 8163 / Rsym value: 0.436 / % possible all: 99.7

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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→24.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.872 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25443 8364 5 %RANDOM
Rwork0.2188 ---
obs0.22062 158213 99.48 %-
all-166992 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.04 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11808 0 108 1586 13502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01912220
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211883
X-RAY DIFFRACTIONr_angle_refined_deg1.3252.02716631
X-RAY DIFFRACTIONr_angle_other_deg0.729327271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47651533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29523.226499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.754151639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7481591
X-RAY DIFFRACTIONr_chiral_restr0.0710.21947
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113516
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022646
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: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 616 -
Rwork0.258 11423 -
obs--99.28 %
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)
10.48540.13970.0650.4214-0.04630.0489-0.0134-0.03090.002-0.03650.014-0.0299-0.0466-0.0545-0.00050.16920.13040.0320.23840.07290.1564109.287-56.44822.1368
21.0541-0.40410.16770.45060.20010.6925-0.00420.0058-0.0021-0.0027-0.06330.02490.04090.00420.06750.15180.16570.03390.22910.06230.165978.3793-51.305-2.5345
30.55790.1778-0.05920.49710.08210.23660.002-0.0072-0.0193-0.01890.00450.0032-0.0207-0.0184-0.00650.1106-0.0239-0.00350.109-0.03160.206739.885-30.575326.2122
40.8134-0.4501-0.2090.7446-0.33331.6855-0.0857-0.07660.01860.0227-0.0338-0.0048-0.01830.3670.11950.12290.0582-0.0040.21050.01140.184770.744-36.179421.4749
50.2514-0.02430.04770.51020.06460.45070.06410.04730.05060.0149-0.0311-0.04570.0798-0.2275-0.0330.132-0.0649-0.03780.24650.05550.1604103.5689-106.410910.1013
61.67560.4267-1.23882.3433-0.79971.10710.03770.0981-0.10490.3306-0.2127-0.21990.1375-0.27940.1750.5708-0.66670.02710.8918-0.02040.03983.5005-130.57115.3105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 400
2X-RAY DIFFRACTION2A401 - 505
3X-RAY DIFFRACTION2A506
4X-RAY DIFFRACTION3B1 - 400
5X-RAY DIFFRACTION4B401 - 505
6X-RAY DIFFRACTION4B506
7X-RAY DIFFRACTION5C1 - 400
8X-RAY DIFFRACTION6C401 - 505
9X-RAY DIFFRACTION6C506

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