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- PDB-8ee0: KS-AT didomain from module 2 of the 6-deoxyerythronolide B syntha... -

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Basic information

Entry
Database: PDB / ID: 8ee0
TitleKS-AT didomain from module 2 of the 6-deoxyerythronolide B synthase in complex with antibody fragment 1B2
Components
  • 1B2 antibody heavy chain
  • 1B2 antibody light chain
  • 6-deoxyerythronolide B synthase
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE/IMMUNE SYSTEM / polyketide synthase / TRANSFERASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
Alpha-Beta Plaits - #3290 / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / 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 ...Alpha-Beta Plaits - #3290 / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / 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 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 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 / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
6-deoxyerythronolide-B synthase
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCogan, D.P. / Brodsky, K.L. / Guzman, K.M. / Mathews, I.I. / Khosla, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141799-02 United States
CitationJournal: Biochemistry / Year: 2023
Title: Discovery and Characterization of Antibody Probes of Module 2 of the 6-Deoxyerythronolide B Synthase.
Authors: Guzman, K.M. / Cogan, D.P. / Brodsky, K.L. / Soohoo, A.M. / Li, X. / Sevillano, N. / Mathews, I.I. / Nguyen, K.P. / Craik, C.S. / Khosla, C.
History
DepositionSep 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-deoxyerythronolide B synthase
L: 1B2 antibody light chain
H: 1B2 antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)149,7653
Polymers149,7653
Non-polymers00
Water2,018112
1
A: 6-deoxyerythronolide B synthase
L: 1B2 antibody light chain
H: 1B2 antibody heavy chain

A: 6-deoxyerythronolide B synthase
L: 1B2 antibody light chain
H: 1B2 antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)299,5306
Polymers299,5306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area17050 Å2
ΔGint-69 kcal/mol
Surface area97430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.850, 91.850, 393.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 6-deoxyerythronolide B synthase / EryAI


Mass: 97601.609 Da / Num. of mol.: 1
Fragment: KS-AT didomain of module 2 (UNP residues 2033-2921)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryAI / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5UNP6, 6-deoxyerythronolide-B synthase
#2: Antibody 1B2 antibody light chain


Mass: 25715.832 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 1B2 antibody heavy chain


Mass: 26447.611 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M lithium chloride, 0.1 M Tris, pH 7, 22.5% PEG8000
PH range: 7

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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: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.65→39.66 Å / Num. obs: 50353 / % possible obs: 99.9 % / Redundancy: 26.252 % / Biso Wilson estimate: 54.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.267 / Rrim(I) all: 0.272 / Χ2: 0.778 / Net I/σ(I): 14.31 / Num. measured all: 1321851 / Scaling rejects: 106
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.7227.492.5111.66100120364236420.6152.558100
2.72-2.7927.4842.089297460354635460.6742.128100
2.79-2.8727.0921.752.4294363348534830.7671.78399.9
2.87-2.9626.6541.4143.189958337633750.8411.441100
2.96-3.0626.2181.0983.9985288325432530.8951.12100
3.06-3.1723.9030.9414.5775725316931680.9090.961100
3.17-3.2927.3720.7226.383594305430540.9610.735100
3.29-3.4227.3750.5328.480921295629560.9820.542100
3.42-3.5727.1560.3911.1276364281328120.9850.398100
3.57-3.7526.9470.32113.4372972271127080.990.32799.9
3.75-3.9526.2350.24416.9668658261826170.9940.249100
3.95-4.1923.760.1820.8258925248024800.9970.184100
4.19-4.4827.4210.14127.3263534231723170.9980.144100
4.48-4.8426.9170.11831.3558760218321830.9980.12100
4.84-5.326.3290.12129.9252790200520050.9980.124100
5.3-5.9324.7050.12927.5345754185718520.9990.13299.7
5.93-6.8424.3970.11629.5540157164616460.9980.118100
6.84-8.3825.4580.07642.5236405143014300.9990.077100
8.38-11.8522.630.04954.54257981142114010.0599.8
11.85-39.6620.8530.04356.7143057206860.9990.04495.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C9U

6c9u


Resolution: 2.65→39.66 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 2513 5 %
Rwork0.2107 47720 -
obs0.2129 50233 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.64 Å2 / Biso mean: 54.9553 Å2 / Biso min: 23.01 Å2
Refinement stepCycle: final / Resolution: 2.65→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9592 0 0 112 9704
Biso mean---49.3 -
Num. residues----1303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.65-2.70.38091380.318626252763
2.7-2.760.39811340.305525412675
2.76-2.820.3871380.28826092747
2.82-2.880.34561370.277926172754
2.88-2.950.30121370.267126032740
2.95-3.030.30911370.254425822719
3.03-3.120.31121370.26326182755
3.12-3.220.34211380.268326062744
3.22-3.340.3231390.249926342773
3.34-3.470.28431370.215726142751
3.47-3.630.24321380.206126392777
3.63-3.820.26171410.205926672808
3.82-4.060.26531390.198426292768
4.06-4.370.1981400.173326712811
4.37-4.810.20621410.158426882829
4.81-5.510.22921420.18426862828
5.51-6.930.24431440.212827592903
6.93-39.660.18341560.182729323088

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