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- PDB-5msv: Structure of the phosphopantetheine modified PCP-R didomain of ca... -

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Basic information

Entry
Database: PDB / ID: 5msv
TitleStructure of the phosphopantetheine modified PCP-R didomain of carboxylic acid reductase (CAR) in complex with NADP
ComponentsThioester reductase domain-containing protein
KeywordsOXIDOREDUCTASE / adenylation domain / carboxylic acid reductase
Function / homology
Function and homology information


long-chain fatty acid-CoA ligase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / biosynthetic process / phosphopantetheine binding / NADP binding / ATP binding / membrane
Similarity search - Function
Carboxylic acid reductase / Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain ...Carboxylic acid reductase / Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 4'-PHOSPHOPANTETHEINE / Carboxylic acid reductase
Similarity search - Component
Biological speciesSegniliparus rugosus ATCC BAA-974 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsGahloth, D. / Leys, D.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structures of carboxylic acid reductase reveal domain dynamics underlying catalysis.
Authors: Gahloth, D. / Dunstan, M.S. / Quaglia, D. / Klumbys, E. / Lockhart-Cairns, M.P. / Hill, A.M. / Derrington, S.R. / Scrutton, N.S. / Turner, N.J. / Leys, D.
History
DepositionJan 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.3Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Thioester reductase domain-containing protein
B: Thioester reductase domain-containing protein
C: Thioester reductase domain-containing protein
D: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)517,88012
Polymers513,4734
Non-polymers4,4078
Water14,232790
1
A: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4703
Polymers128,3681
Non-polymers1,1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4703
Polymers128,3681
Non-polymers1,1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4703
Polymers128,3681
Non-polymers1,1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4703
Polymers128,3681
Non-polymers1,1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.110, 92.110, 363.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA669 - 1187669 - 1187
21PROPROLEULEUBB669 - 1187669 - 1187
12PROPROLEULEUAA669 - 1188669 - 1188
22PROPROLEULEUCC669 - 1188669 - 1188
13PROPROGLYGLYAA669 - 1186669 - 1186
23PROPROGLYGLYDD669 - 1186669 - 1186
14ARGARGLEULEUBB668 - 1187668 - 1187
24ARGARGLEULEUCC668 - 1187668 - 1187
15ARGARGLEULEUBB668 - 1187668 - 1187
25ARGARGLEULEUDD668 - 1187668 - 1187
16ARGARGLEULEUCC668 - 1187668 - 1187
26ARGARGLEULEUDD668 - 1187668 - 1187

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Thioester reductase domain-containing protein


Mass: 128368.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Segniliparus rugosus ATCC BAA-974 (bacteria)
Gene: HMPREF9336_01297 / Production host: Escherichia coli (E. coli) / References: UniProt: E5XP76
#2: Chemical
ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: CARsr PCP-Red crystals were obtained in 0.1 M carboxylic acids 0.1M, Buffer system 1 pH 6.5, 50% Precipitant Mix 2 of Morpheus screen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.34→200 Å / Num. obs: 120649 / % possible obs: 95 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.3
Reflection shellResolution: 2.34→2.42 Å / CC1/2: 0.5 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MSO

5mso


Resolution: 2.34→200 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.494 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 5923 4.9 %RANDOM
Rwork0.19143 ---
obs0.19223 114730 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 44.473 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.53 Å20 Å2
3---1.06 Å2
Refinement stepCycle: 1 / Resolution: 2.34→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15747 0 244 790 16781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01916347
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215489
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.97622265
X-RAY DIFFRACTIONr_angle_other_deg1.269335566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28252045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42223.764728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.759152518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.60715111
X-RAY DIFFRACTIONr_chiral_restr0.0750.22526
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118509
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023706
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_it2.3492.8378216
X-RAY DIFFRACTIONr_mcbond_other2.3482.8378215
X-RAY DIFFRACTIONr_mcangle_it3.5294.24810249
X-RAY DIFFRACTIONr_mcangle_other3.5294.24710250
X-RAY DIFFRACTIONr_scbond_it3.2833.1378131
X-RAY DIFFRACTIONr_scbond_other3.2833.1378130
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1484.56812016
X-RAY DIFFRACTIONr_long_range_B_refined6.48122.53718317
X-RAY DIFFRACTIONr_long_range_B_other6.4822.53718317
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)
11A616920.07
12B616920.07
21A621060.06
22C621060.06
31A619240.06
32D619240.06
41B618520.07
42C618520.07
51B620240.07
52D620240.07
61C624040.06
62D624040.06
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 348 -
Rwork0.309 7424 -
obs--82.96 %
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)
10.8786-0.2205-0.03871.4838-0.03620.6869-0.0424-0.03080.11010.21030.04680.0179-0.11190.0019-0.00450.09350.00930.05620.00230.00050.08125.0890.42429.733
21.4946-0.1767-0.5630.58620.040.82290.12230.2960.133-0.0254-0.02720.0389-0.1016-0.2523-0.09520.03480.04940.02340.15930.11530.111523.88992.733-19.499
30.7024-0.50060.09541.6524-0.26450.7019-0.0876-0.0646-0.27930.18030.13580.15170.0028-0.0075-0.04830.06450.01790.08980.02780.04830.241435.46445.49939.489
41.60330.0245-0.34030.6489-0.06680.92830.02280.06230.0233-0.00230.0144-0.10830.00060.0713-0.03710.0231-0.0120.01360.03720.0330.14768.89884.008-30.476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A669 - 1188
2X-RAY DIFFRACTION2B668 - 1187
3X-RAY DIFFRACTION3C668 - 1188
4X-RAY DIFFRACTION4D668 - 1187

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