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- PDB-8ee1: KS-AT didomain from module 2 of the 6-deoxyerythronolide B syntha... -

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Basic information

Entry
Database: PDB / ID: 8ee1
TitleKS-AT didomain from module 2 of the 6-deoxyerythronolide B synthase in complex with antibody fragment AA5
Components
  • 6-deoxyerythronolide B synthase
  • AA5 antibody heavy chain
  • AA5 antibody light chain
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE/IMMUNE SYSTEM / polyketide synthase / TRANSFERASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
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 ...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 domain superfamily
Similarity search - Domain/homology
Biological speciesSaccharopolyspora erythraea (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-deoxyerythronolide B synthase
B: AA5 antibody heavy chain
C: AA5 antibody light chain
D: 6-deoxyerythronolide B synthase
G: AA5 antibody heavy chain
H: AA5 antibody light chain


Theoretical massNumber of molelcules
Total (without water)298,3486
Polymers298,3486
Non-polymers00
Water1,33374
1
A: 6-deoxyerythronolide B synthase
B: AA5 antibody heavy chain
C: AA5 antibody light chain

D: 6-deoxyerythronolide B synthase
G: AA5 antibody heavy chain
H: AA5 antibody light chain


Theoretical massNumber of molelcules
Total (without water)298,3486
Polymers298,3486
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)249.370, 252.440, 63.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein 6-deoxyerythronolide B synthase / EryAI


Mass: 97601.609 Da / Num. of mol.: 2
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
#2: Antibody AA5 antibody heavy chain


Mass: 26334.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Antibody AA5 antibody light chain


Mass: 25238.037 Da / Num. of mol.: 2
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 / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Morpheus reagents (0.1 M Carboxylic Acids Mix, 0.1 M Buffer System 2, pH 7.0, 30.6 % v/v Precipitant Mix 2), Silver bullet reagents (0.004 M cadmium chloride hydrate, 0.004 M cobalt(II) ...Details: Morpheus reagents (0.1 M Carboxylic Acids Mix, 0.1 M Buffer System 2, pH 7.0, 30.6 % v/v Precipitant Mix 2), Silver bullet reagents (0.004 M cadmium chloride hydrate, 0.004 M cobalt(II) chloride hexahydrate, 0.004 M copper(II) chloride dihydrate, 0.004 nickel(II) chloride hexahydrate, 0.02 M HEPES sodium, pH 6.8)
PH range: 6.8-7

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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 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.7→39.62 Å / Num. obs: 110267 / % possible obs: 98.3 % / Redundancy: 27.077 % / Biso Wilson estimate: 73.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.165 / Χ2: 0.846 / Net I/σ(I): 17.97 / Num. measured all: 2985709 / Scaling rejects: 1314
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
2.7-2.7726.3222.9911.66214185824781370.5993.04998.7
2.77-2.8526.0482.412.03193851788974420.6942.45894.3
2.85-2.9328.3321.7322.98220618783277870.8111.76399.4
2.93-3.0228.5151.3173.8213752752574960.8861.34199.6
3.02-3.1228.2921.0534.68205515730272640.9171.07299.5
3.12-3.2327.8840.7816.24197109712070690.9510.79699.3
3.23-3.3527.5980.5428.68188353685268250.9740.55299.6
3.35-3.4927.4090.38211.72178293656565050.9880.38999.1
3.49-3.6425.7680.27614.86159376635161850.9920.28197.4
3.64-3.8227.2670.20918.83158969607758300.9960.21395.9
3.82-4.0228.2330.15624.22163551581557930.9970.15999.6
4.02-4.2727.6380.12228.89151458549754800.9980.12599.7
4.27-4.5626.9420.09933.79138536516851420.9980.10199.5
4.56-4.9326.320.09135.45126520483348070.9990.09399.5
4.93-5.424.60.08834.19104944444542660.9990.0996
5.4-6.0426.9420.08637.18105289403439080.9990.08896.9
6.04-6.9726.970.07343.0197549362936170.9990.07599.7
6.97-8.5425.870.05652.0478696307730420.9990.05898.9
8.54-12.0724.0550.04662.1554725243822750.9990.04793.3
12.07-39.6224.6390.04168.94344201452139710.04296.2

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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: 2.7→39.62 Å / SU ML: 0.4169 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2538 5510 5 %
Rwork0.2248 104707 -
obs0.2262 110217 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.56 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17684 0 0 74 17758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010518051
X-RAY DIFFRACTIONf_angle_d1.264724593
X-RAY DIFFRACTIONf_chiral_restr0.07162784
X-RAY DIFFRACTIONf_plane_restr0.0253255
X-RAY DIFFRACTIONf_dihedral_angle_d18.08626333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.46911830.40073485X-RAY DIFFRACTION99.27
2.73-2.760.40031820.3823448X-RAY DIFFRACTION98.27
2.76-2.80.39451710.35983275X-RAY DIFFRACTION92.98
2.8-2.830.39881700.33053237X-RAY DIFFRACTION93.44
2.83-2.870.36151820.30693470X-RAY DIFFRACTION99.46
2.87-2.910.30431870.28683548X-RAY DIFFRACTION99.2
2.91-2.950.34721810.27343446X-RAY DIFFRACTION99.97
2.95-2.990.30561840.26993488X-RAY DIFFRACTION99.46
2.99-3.040.29161870.27273543X-RAY DIFFRACTION99.36
3.04-3.090.28941800.26893433X-RAY DIFFRACTION99.45
3.09-3.140.32111850.27893505X-RAY DIFFRACTION99.49
3.14-3.20.311860.26973533X-RAY DIFFRACTION99.36
3.2-3.260.2951810.26823456X-RAY DIFFRACTION99.64
3.26-3.330.30641850.28063509X-RAY DIFFRACTION99.41
3.33-3.40.31951840.26663493X-RAY DIFFRACTION99.24
3.4-3.480.28121840.23593489X-RAY DIFFRACTION99.19
3.48-3.570.26471860.23273536X-RAY DIFFRACTION99.02
3.57-3.660.25121710.22943245X-RAY DIFFRACTION93.03
3.66-3.770.27331830.22393491X-RAY DIFFRACTION96.74
3.77-3.890.24391820.22763461X-RAY DIFFRACTION99.62
3.89-4.030.22591880.2123556X-RAY DIFFRACTION99.81
4.03-4.190.23751850.19893527X-RAY DIFFRACTION99.6
4.19-4.380.22251870.18843537X-RAY DIFFRACTION99.57
4.38-4.610.20811880.17483579X-RAY DIFFRACTION99.66
4.62-4.90.22941870.19353555X-RAY DIFFRACTION99.36
4.9-5.280.2411870.20153544X-RAY DIFFRACTION98.7
5.28-5.810.26331780.21693398X-RAY DIFFRACTION93.76
5.81-6.650.26911880.22083565X-RAY DIFFRACTION99.26
6.65-8.360.19441920.19323658X-RAY DIFFRACTION99.07
8.36-39.620.20981960.21023697X-RAY DIFFRACTION95.67

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