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- PDB-6h1b: Structure of amide bond synthetase Mcba K483A mutant from Marinac... -

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Basic information

Entry
Database: PDB / ID: 6h1b
TitleStructure of amide bond synthetase Mcba K483A mutant from Marinactinospora thermotolerans
ComponentsFatty acid CoA ligase
KeywordsLIGASE / McbA / amide / ATP / ANL enzyme
Function / homology
Function and homology information


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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme ...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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Chem-EQ2 / Fatty acid CoA ligase
Similarity search - Component
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRowlinson, B. / Petchey, M. / Cuetos, A. / Frese, A. / Dannevald, S. / Grogan, G.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: The Broad Aryl Acid Specificity of the Amide Bond Synthetase McbA Suggests Potential for the Biocatalytic Synthesis of Amides.
Authors: Petchey, M. / Cuetos, A. / Rowlinson, B. / Dannevald, S. / Frese, A. / Sutton, P.W. / Lovelock, S. / Lloyd, R.C. / Fairlamb, I.J.S. / Grogan, G.
History
DepositionJul 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_PDB_obs_spr / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 8, 2023Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid CoA ligase
B: Fatty acid CoA ligase
C: Fatty acid CoA ligase
D: Fatty acid CoA ligase
E: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,09915
Polymers266,0915
Non-polymers3,00710
Water3,495194
1
A: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.234, 130.738, 196.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHRAA-1 - 4943 - 498
21PROPROTHRTHRBB-1 - 4943 - 498
12PROPROTHRTHRAA-1 - 4943 - 498
22PROPROTHRTHRCC-1 - 4943 - 498
13PROPROTHRTHRAA-1 - 4943 - 498
23PROPROTHRTHRDD-1 - 4943 - 498
14METMETTHRTHRAA1 - 4945 - 498
24METMETTHRTHREE1 - 4945 - 498
15PROPROTHRTHRBB-1 - 4943 - 498
25PROPROTHRTHRCC-1 - 4943 - 498
16PROPROTHRTHRBB-1 - 4943 - 498
26PROPROTHRTHRDD-1 - 4943 - 498
17METMETTHRTHRBB1 - 4945 - 498
27METMETTHRTHREE1 - 4945 - 498
18PROPROTHRTHRCC-1 - 4943 - 498
28PROPROTHRTHRDD-1 - 4943 - 498
19METMETASPASPCC1 - 4955 - 499
29METMETASPASPEE1 - 4955 - 499
110METMETTHRTHRDD1 - 4945 - 498
210METMETTHRTHREE1 - 4945 - 498

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Fatty acid CoA ligase


Mass: 53218.293 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinactinospora thermotolerans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: R4R1U5
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-EQ2 / 1-ethanoyl-9~{H}-pyrido[3,4-b]indole-3-carboxylic acid


Mass: 254.241 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C14H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1. 6 M sodium citrate

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.8→108.83 Å / Num. obs: 75674 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.11 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.86 Å / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.67 / Rpim(I) all: 0.46

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GXQ

4gxq


Resolution: 2.8→101.5 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.899 / SU B: 16.689 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24775 3618 4.8 %RANDOM
Rwork0.20396 ---
obs0.20605 71980 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.194 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å2-0 Å2-0 Å2
2--1.97 Å2-0 Å2
3----4.66 Å2
Refinement stepCycle: 1 / Resolution: 2.8→101.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17686 0 206 196 18088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01418329
X-RAY DIFFRACTIONr_bond_other_d0.0020.01716365
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.66125137
X-RAY DIFFRACTIONr_angle_other_deg0.8791.6337975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg752422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35419.658819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.645152487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3315158
X-RAY DIFFRACTIONr_chiral_restr0.0630.22458
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023280
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_it4.4125.1579730
X-RAY DIFFRACTIONr_mcbond_other4.4125.1579729
X-RAY DIFFRACTIONr_mcangle_it6.7987.72712132
X-RAY DIFFRACTIONr_mcangle_other6.7977.72812133
X-RAY DIFFRACTIONr_scbond_it4.4795.3198599
X-RAY DIFFRACTIONr_scbond_other4.4795.3198600
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8577.87713004
X-RAY DIFFRACTIONr_long_range_B_refined9.79260.48119286
X-RAY DIFFRACTIONr_long_range_B_other9.79260.4819287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A143180.06
12B143180.06
21A143730.06
22C143730.06
31A144770.06
32D144770.06
41A137060.09
42E137060.09
51B142910.06
52C142910.06
61B143660.05
62D143660.05
71B135830.09
72E135830.09
81C143470.06
82D143470.06
91C135970.09
92E135970.09
101D136150.09
102E136150.09
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 282 -
Rwork0.327 5258 -
obs--100 %

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