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- PDB-6w7s: Ketoreductase from module 1 of the 6-deoxyerythronolide B synthas... -

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Basic information

Entry
Database: PDB / ID: 6w7s
TitleKetoreductase from module 1 of the 6-deoxyerythronolide B synthase (KR1) in complex with antibody fragment (Fab) 2G10
Components
  • 2G10 (Fab heavy chain)
  • 2G10 (Fab light chain)
  • EryAI
KeywordsOXIDOREDUCTASE/IMMUNE SYSTEM / ketoreductase / antibody fragment / OXIDOREDUCTASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
CurL-like, PKS C-terminal / PKS_PP_betabranch / : / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase ...CurL-like, PKS C-terminal / PKS_PP_betabranch / : / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Erythronolide synthase EryA1 / 6-deoxyerythronolide-B synthase
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCogan, D.P. / Mathews, I.I. / Khosla, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087934 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Antibody Probes of Module 1 of the 6-Deoxyerythronolide B Synthase Reveal an Extended Conformation During Ketoreduction.
Authors: Cogan, D.P. / Li, X. / Sevillano, N. / Mathews, I.I. / Matsui, T. / Craik, C.S. / Khosla, C.
History
DepositionMar 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EryAI
H: 2G10 (Fab heavy chain)
L: 2G10 (Fab light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5325
Polymers103,3023
Non-polymers2312
Water7,548419
1
H: 2G10 (Fab heavy chain)
L: 2G10 (Fab light chain)
hetero molecules

A: EryAI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5325
Polymers103,3023
Non-polymers2312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545x+1/2,y-1/2,z1
Buried area5460 Å2
ΔGint-35 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.148, 129.532, 208.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein EryAI


Mass: 50888.957 Da / Num. of mol.: 1 / Fragment: module 1 (UNP residues 1448-1928)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryAI / Plasmid: pAYC59 / Production host: Escherichia coli (E. coli) / Strain (production host): BAP1 / References: UniProt: Q5UNP6, UniProt: Q03131*PLUS

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Antibody , 2 types, 2 molecules HL

#2: Antibody 2G10 (Fab heavy chain)


Mass: 27107.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Antibody 2G10 (Fab light chain)


Mass: 25305.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 3 types, 421 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 15% PEG6000, 5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.249→39.36 Å / Num. obs: 51949 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.075 / Rrim(I) all: 0.281 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.3213.92.0066161244190.6810.5542.0821.699.2
9.27-39.36130.058106878240.9990.0170.062998.9

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Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FR0

2fr0


Resolution: 2.25→39.36 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 2616 5.04 %
Rwork0.1793 49278 -
obs0.1819 51894 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.08 Å2 / Biso mean: 36.4821 Å2 / Biso min: 13.92 Å2
Refinement stepCycle: final / Resolution: 2.25→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6666 0 13 426 7105
Biso mean--38.96 37.8 -
Num. residues----897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.290.28591280.25622533266199
2.29-2.330.31911340.254625382672100
2.33-2.380.30741250.242826032728100
2.38-2.430.29031460.231325582704100
2.43-2.490.3021400.216225692709100
2.49-2.550.2541280.206225572685100
2.55-2.620.25831490.197225882737100
2.62-2.70.23531520.194625422694100
2.7-2.780.26761390.194325662705100
2.79-2.880.29721440.20225622706100
2.88-30.25481200.189826062726100
3-3.140.2851040.190926132717100
3.14-3.30.21161240.189826292753100
3.3-3.510.21671570.170325752732100
3.51-3.780.21651370.166826062743100
3.78-4.160.2011420.152326042746100
4.16-4.760.19051780.132726022780100
4.76-5.990.18421270.156926582785100
5.99-39.360.21871420.168827692911100

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