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- PDB-5xww: Substrate-bound Structure of G355T/Q364H mutant of a Ketoreductas... -

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Basic information

Entry
Database: PDB / ID: 5xww
TitleSubstrate-bound Structure of G355T/Q364H mutant of a Ketoreductase from amphotericin Polyketide Synthases
ComponentsAmphB
KeywordsOXIDOREDUCTASE / modular polyketide synthease / ketoreductase / mutant
Function / homology
Function and homology information


macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / nucleotide binding / identical protein binding
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Thiolase-like / 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
Chem-8H6 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / AmphB
Similarity search - Component
Biological speciesStreptomyces nodosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLiu, C. / Zheng, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Program on Key Basic Research Project2013CB734002 China
National Natural Science Foundation of China31370101 China
National Natural Science Foundation of China31570056 China
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Substrate-bound structures of a ketoreductase from amphotericin modular polyketide synthase.
Authors: Liu, C. / Yuan, M. / Xu, X. / Wang, L. / Keatinge-Clay, A.T. / Deng, Z. / Lin, S. / Zheng, J.
History
DepositionJun 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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: AmphB
B: AmphB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2256
Polymers102,9582
Non-polymers2,2684
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-12 kcal/mol
Surface area34480 Å2
Unit cell
Length a, b, c (Å)61.066, 63.627, 71.586
Angle α, β, γ (deg.)72.67, 67.21, 89.88
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: -3 - 473 / Label seq-ID: 18 - 494

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein AmphB


Mass: 51478.766 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2529-3003 / Mutation: G355T, Q364H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nodosus (bacteria) / Gene: amphB / Production host: Escherichia coli (E. coli) / References: UniProt: Q93NW7
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-8H6 / S-[2-[3-[[(2R)-3,3-dimethyl-2,4-bis(oxidanyl)butanoyl]amino]propanoylamino]ethyl] (2R)-2-methyl-3-oxidanylidene-pentanethioate


Mass: 390.495 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H30N2O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 3.4 M ammonium sulfate, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.96→62.48 Å / Num. obs: 63286 / % possible obs: 94.6 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2 / Num. unique obs: 3033 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MJE

3mje


Resolution: 1.96→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.716 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21656 3200 5.1 %RANDOM
Rwork0.1803 ---
obs0.18214 60085 94.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.437 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20.11 Å2
2---0.55 Å2-0.9 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.96→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6946 0 148 102 7196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197242
X-RAY DIFFRACTIONr_bond_other_d00.026892
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9839910
X-RAY DIFFRACTIONr_angle_other_deg0.58315762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09522.867286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5161564
X-RAY DIFFRACTIONr_chiral_restr0.0620.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0218328
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021604
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_it2.7912.6753814
X-RAY DIFFRACTIONr_mcbond_other2.7912.6743813
X-RAY DIFFRACTIONr_mcangle_it3.7893.9924764
X-RAY DIFFRACTIONr_mcangle_other3.7893.9934765
X-RAY DIFFRACTIONr_scbond_it4.1043.2063428
X-RAY DIFFRACTIONr_scbond_other4.1043.2063429
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2184.6055147
X-RAY DIFFRACTIONr_long_range_B_refined8.2152.07830811
X-RAY DIFFRACTIONr_long_range_B_other8.21352.08730766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28478 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.963→2.014 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 202 -
Rwork0.227 4089 -
obs--86.23 %
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)
10.0924-0.0151-0.02170.26480.10530.10030.00210.0039-0.01250.01010.005-0.0177-0.0121-0.0007-0.00710.0193-0.0024-0.00370.01610.00470.0056-10.2922.0917-17.0972
20.07840.0057-0.00140.24370.08880.1155-0.0023-0.00610.008-0.01180.0012-0.01570.0045-0.00730.00110.02510.0024-0.00210.00790.00180.0051-13.0296-16.364223.6962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 473
2X-RAY DIFFRACTION2B-3 - 473

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