[English] 日本語
Yorodumi
- PDB-2qec: Crystal structure of histone acetyltransferase HPA2 and related a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qec
TitleCrystal structure of histone acetyltransferase HPA2 and related acetyltransferase (NP_600742.1) from Corynebacterium glutamicum ATCC 13032 at 1.90 A resolution
ComponentsHistone acetyltransferase HPA2 and related acetyltransferases
KeywordsTRANSFERASE / NP_600742.1 / histone acetyltransferase HPA2 and related acetyltransferase / Acetyltransferase (GNAT) family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone acetyltransferase HPA2 and related acetyltransferases
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / MAD / molecular replacement / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of histone acetyltransferase HPA2 and related acetyltransferase (NP_600742.1) from Corynebacterium glutamicum ATCC 13032 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone acetyltransferase HPA2 and related acetyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,81410
Polymers22,2561
Non-polymers5599
Water2,720151
1
A: Histone acetyltransferase HPA2 and related acetyltransferases
hetero molecules

A: Histone acetyltransferase HPA2 and related acetyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,62820
Polymers44,5112
Non-polymers1,11718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5330 Å2
ΔGint27 kcal/mol
Surface area18650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.070, 79.070, 181.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION

-
Components

#1: Protein Histone acetyltransferase HPA2 and related acetyltransferases / GCN5-related N-acetyltransferase


Mass: 22255.531 Da / Num. of mol.: 1 / Mutation: A29T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025 / Gene: NP_600742.1, Cgl1527, cg1722 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8NQB1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE. 2. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATION: A29T.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.6766.5DATA FROM A SE-MET CONTAINING CRYSTAL IN SPACEGROUP P6(2)22 WAS USED FOR THE MAD PHASING EXPERIMENTS AT 2.30 ANGSTROM RESOLUTION. THIS MAD STRUCTURE WAS USED AS A MOLECULAR REPLACEMENT MODEL TO PHASE THIS STRUCTURE AT 1.90 ANGSTROM RESOLUTION IN THE P6(5)22 SPACEGROUP.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop4.6NANODROP, 8.0% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop8.5NANODROP, 0.2M Li2SO4, 40.0% PEG 400, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.91162
SYNCHROTRONSSRL BL11-120.97917, 0.91837, 0.97886
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJan 18, 2007Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDJan 7, 2007Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal Si(111) bent (horizontal focusing)SINGLE WAVELENGTHMx-ray1
2Single crystal Si(111) bent (horizontal focusing)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979171
30.918371
40.978861
ReflectionResolution: 1.9→27.64 Å / Num. obs: 27197 / % possible obs: 99.5 % / Redundancy: 17.62 % / Biso Wilson estimate: 32.59 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.36
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.9-1.970.9052290601,299.3
1.97-2.050.6242.8291341,299
2.05-2.140.4224275731,299.3
2.14-2.250.4115.9472271,299.5
2.25-2.390.3338.3570391,299.4
2.39-2.580.22611.7594951,299.6
2.58-2.840.14417.3578361,299.8
2.84-3.250.08627.1579131,299.8
3.25-4.080.05142563761,299.9
4.08-27.640.03651.7574591,299.5

-
Phasing

Phasing
Method
MAD
molecular replacement

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
Blu-Icev 5.0data collection
XDSdata reduction
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
autoSHARPphasing
PHASERphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.9→27.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.388 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ETHYLENE GLYCOL WAS MODELED BASED ON CRYO CONDITIONS. 5. RESIDUES 83-94, 103, 107-115 ARE DISORDERED AND WERE NOT MODELED. 6. ASP 186 IS A RAMACHANDRAN OUTLIER AND IS LOCATED IN POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1363 5 %RANDOM
Rwork0.193 ---
all0.195 ---
obs0.195 27120 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.353 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20.89 Å20 Å2
2--1.77 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 36 151 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221457
X-RAY DIFFRACTIONr_bond_other_d0.0010.021357
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9751977
X-RAY DIFFRACTIONr_angle_other_deg1.09533139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5295183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36623.15857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39115206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.97159
X-RAY DIFFRACTIONr_chiral_restr0.1490.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02290
X-RAY DIFFRACTIONr_nbd_refined0.2250.2286
X-RAY DIFFRACTIONr_nbd_other0.1870.21311
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2691
X-RAY DIFFRACTIONr_nbtor_other0.0860.2834
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0370.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.213
X-RAY DIFFRACTIONr_mcbond_it2.373942
X-RAY DIFFRACTIONr_mcbond_other0.6033363
X-RAY DIFFRACTIONr_mcangle_it3.61351471
X-RAY DIFFRACTIONr_scbond_it5.48601
X-RAY DIFFRACTIONr_scangle_it7.14211503
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 87 -
Rwork0.285 1843 -
obs-1930 99.13 %
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)
11.5341-0.17421.03680.57470.68673.97420.0749-0.04920.0814-0.2093-0.2460.2036-0.1457-0.31690.1711-0.01480.0085-0.0784-0.2175-0.0622-0.147814.85126.0134.503
20.63850.4625-0.04444.13581.76651.78190.0320.1007-0.0192-0.3209-0.0852-0.0303-0.2008-0.13110.05320.0135-0.0208-0.0382-0.23290.0157-0.176721.75411.2450.638
320.158520.54627.490349.728324.380949.3682-0.0307-0.9469-0.88572.894-0.85031.79721.8854-2.71260.8810.68110.0576-0.00520.8726-0.0930.7619-1.61622.7642.037
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 822 - 83
22117 - 203118 - 204
3395 - 10696 - 107

+
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://pdbjlvh1.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