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- PDB-5msr: Structure of the unmodified PCP-R domain of carboxylic acid reduc... -

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Basic information

Entry
Database: PDB / ID: 5msr
TitleStructure of the unmodified PCP-R domain of carboxylic acid reductase (CAR) from Segniliparus rugosus in complex with NADPH, P43 form
ComponentsThioester reductase domain-containing protein
KeywordsOXIDOREDUCTASE / adenylation domain / carboxylic acid reductase
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / organonitrogen compound biosynthetic process / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / phosphopantetheine binding / lipid metabolic process / NADP binding / ATP binding
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. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase ...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. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / 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 / Carboxylic acid reductase
Similarity search - Component
Biological speciesSegniliparus rugosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)516,4468
Polymers513,4734
Non-polymers2,9744
Water4,197233
1
A: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1122
Polymers128,3681
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1122
Polymers128,3681
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1122
Polymers128,3681
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1122
Polymers128,3681
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.943, 94.943, 335.506
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: 0 / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA666 - 1187666 - 1187
21GLYGLYBB666 - 1187666 - 1187
12GLYGLYAA666 - 1187666 - 1187
22GLYGLYCC666 - 1187666 - 1187
13ARGARGAA668 - 1187668 - 1187
23ARGARGDD668 - 1187668 - 1187
14GLYGLYBB666 - 1187666 - 1187
24GLYGLYCC666 - 1187666 - 1187
15ARGARGBB668 - 1187668 - 1187
25ARGARGDD668 - 1187668 - 1187
16ARGARGCC668 - 1187668 - 1187
26ARGARGDD668 - 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 (bacteria) / Gene: HMPREF9336_01297 / Production host: Escherichia coli (E. coli) / References: UniProt: E5XP76
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


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


Mass: 18.015 Da / Num. of mol.: 233 / 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 the condition 0.1 M sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0.5% Jeffamine ED-2003.

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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: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.37→200 Å / Num. obs: 112379 / % possible obs: 99 % / Redundancy: 5.6 % / CC1/2: 1 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.4
Reflection shellResolution: 2.37→2.46 Å / CC1/2: 0.5 / % possible all: 99.5

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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: 2.37→200 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.025 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.221 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24127 5667 4.8 %RANDOM
Rwork0.21869 ---
obs0.2198 112379 98.65 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 86.534 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.37→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15712 0 160 233 16105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01916226
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215388
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.97122109
X-RAY DIFFRACTIONr_angle_other_deg1.258335334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15252041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89523.707723
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.037152512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.36815112
X-RAY DIFFRACTIONr_chiral_restr0.080.22514
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118401
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023683
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_it4.6626.0458203
X-RAY DIFFRACTIONr_mcbond_other4.6616.0468202
X-RAY DIFFRACTIONr_mcangle_it6.9499.06710231
X-RAY DIFFRACTIONr_mcangle_other6.9489.06710232
X-RAY DIFFRACTIONr_scbond_it5.0536.4288023
X-RAY DIFFRACTIONr_scbond_other5.0546.4288022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.869.46211878
X-RAY DIFFRACTIONr_long_range_B_refined10.57547.45417378
X-RAY DIFFRACTIONr_long_range_B_other10.57547.45417379
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)
11A610320.07
12B610320.07
21A615080.06
22C615080.06
31A598080.07
32D598080.07
41B614320.07
42C614320.07
51B595240.08
52D595240.08
61C601560.07
62D601560.07
LS refinement shellResolution: 2.37→2.431 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 416 -
Rwork0.359 8365 -
obs--98.92 %
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)
11.5607-0.931-0.1491.41510.0230.97250.07860.0192-0.03270.0553-0.05470.2659-0.0543-0.2419-0.0240.10190.0259-0.00960.1685-0.08310.1367-55.615130.70234.778
21.2714-0.0028-0.37030.97680.20421.4668-0.0461-0.1231-0.14750.03470.0846-0.1911-0.0060.2501-0.03850.13420.0167-0.02080.1215-0.07680.1206-31.77491.75310.927
32.01980.56280.92630.89430.15962.05480.020.2773-0.0595-0.00510.1014-0.24370.0940.5074-0.12140.0950.0669-0.02150.2089-0.10180.125-9.933122.25745.569
42.680.9931-0.4961.9185-0.17161.51110.02860.03720.26830.08980.00280.4327-0.0814-0.2324-0.03130.14610.11170.02440.1406-0.0560.2066-77.3983.91822.237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A666 - 1187
2X-RAY DIFFRACTION2B666 - 1187
3X-RAY DIFFRACTION3C666 - 1187
4X-RAY DIFFRACTION4D668 - 1187

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