[English] 日本語
Yorodumi
- PDB-8ee1: KS-AT didomain from module 2 of the 6-deoxyerythronolide B syntha... -

+
Open data


ID or keywords:

Loading...

-
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


erythronolide synthase activity / 6-deoxyerythronolide-B synthase / 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 / 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 / NAD(P)-binding domain superfamily / Immunoglobulins / Immunoglobulin-like / 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: 2.7 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more