[English] 日本語
Yorodumi
- PDB-3bv8: Crystal structure of the N-terminal domain of tetrahydrodipicolin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bv8
TitleCrystal structure of the N-terminal domain of tetrahydrodipicolinate acetyltransferase from Staphylococcus aureus
ComponentsTetrahydrodipicolinate acetyltransferase
KeywordsTRANSFERASE / acetyltransferase / pfam08503 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


tetrahydrodipicolinate N-acetyltransferase / tetrahydrodipicolinate N-acetyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate
Similarity search - Function
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, N-terminal / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, DapH / Tetrahydrodipicolinate succinyltransferase N-terminal / Malonyl-CoA ACP transacylase, ACP-binding / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily ...2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, N-terminal / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, DapH / Tetrahydrodipicolinate succinyltransferase N-terminal / Malonyl-CoA ACP transacylase, ACP-binding / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsCuff, M.E. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the N-terminal domain of tetrahydrodipicolinate acetyltransferase from Staphylococcus aureus.
Authors: Cuff, M.E. / Duggan, E. / Clancy, S. / Joachimiak, A.
History
DepositionJan 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tetrahydrodipicolinate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2123
Polymers10,0971
Non-polymers1152
Water2,684149
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Tetrahydrodipicolinate acetyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)61,27318
Polymers60,5826
Non-polymers69112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.503, 76.503, 93.862
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-103-

HOH

21A-111-

HOH

31A-113-

HOH

41A-152-

HOH

51A-236-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Components

#1: Protein Tetrahydrodipicolinate acetyltransferase


Mass: 10097.082 Da / Num. of mol.: 1 / Fragment: N-terminal domain: Residues 5-88 / Mutation: S20F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: Mu50 / Gene: dapD, SAV1397 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7A2S0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Sodium malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921, 0.97942
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 5, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979421
ReflectionResolution: 1.75→50 Å / Num. all: 16945 / Num. obs: 16945 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.78 / Net I/σ(I): 10.3
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1105 / Χ2: 0.924 / % possible all: 100

-
Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.75 Å / D res low: 50 Å / FOM : 0.447 / FOM acentric: 0.48 / FOM centric: 0.285 / Reflection: 16823 / Reflection acentric: 13940 / Reflection centric: 2883
Phasing MAD set

Highest resolution: 1.75 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
12.3810.20.100139402883
20.890.846.28.60.720.58138982870
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
111.24-501.1410.30.2002852
16.33-11.241.9810.50.200195149
14.41-6.331.5610.40.200531231
13.38-4.411.1910.30.2001013313
12.74-3.381.810.30.1001681409
12.31-2.742.7110.20.1002479494
11.99-2.313.0110.20.1003457582
11.75-1.995.2410.20004556653
211.24-500.740.6756.22.921.452850
26.33-11.240.570.575.26.92.281.73195149
24.41-6.330.620.655.67.51.921.31531228
23.38-4.410.750.755.98.21.440.881012311
22.74-3.380.780.755.381.230.771681409
22.31-2.740.880.885.78.20.840.482477491
21.99-2.310.970.926.19.10.540.363448581
21.75-1.990.990.98710.10.330.24526651
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se25.54709-0.524-0.176-0.2150
2Se25.70739-0.524-0.177-0.215-0.138
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
11.24-500.6060.8650.466802852
6.33-11.240.7390.8250.627344195149
4.41-6.330.730.8120.542762531231
3.38-4.410.6560.7350.413261013313
2.74-3.380.6250.6790.40320901681409
2.31-2.740.5260.5820.24629732479494
1.99-2.310.3950.4290.18940393457582
1.75-1.990.2540.2780.08652094556653
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 16823
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.96-10037.70.891503
4.67-5.9629.20.942502
4.03-4.6736.50.949514
3.65-4.03370.94505
3.37-3.6535.30.931513
3.17-3.3733.10.947501
3-3.1738.60.93522
2.86-342.70.925520
2.74-2.8640.30.913543
2.63-2.7446.10.89555
2.54-2.6344.30.878583
2.45-2.5448.10.86608
2.37-2.4549.40.864616
2.3-2.3751.80.857635
2.24-2.354.20.838657
2.18-2.2454.50.848667
2.12-2.1852.60.828699
2.07-2.1262.20.849704
2.02-2.0760.20.836731
1.98-2.0261.10.848748
1.94-1.9864.50.815763
1.9-1.9464.50.805765
1.86-1.966.40.772778
1.83-1.8671.70.749780
1.79-1.8371.80.732810
1.75-1.7974.70.7041101

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.66 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.239 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.086
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 854 5.1 %RANDOM
Rwork0.175 ---
all0.176 16822 --
obs0.176 16822 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.855 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.47 Å20 Å2
2--0.93 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms695 0 7 149 851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022835
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9631140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27625.95242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7115153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.59152
X-RAY DIFFRACTIONr_chiral_restr0.10.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02665
X-RAY DIFFRACTIONr_nbd_refined0.2210.2376
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2114
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.240
X-RAY DIFFRACTIONr_mcbond_it0.7331.5500
X-RAY DIFFRACTIONr_mcangle_it1.3892826
X-RAY DIFFRACTIONr_scbond_it2.3053345
X-RAY DIFFRACTIONr_scangle_it3.8044.5314
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 60 -
Rwork0.286 1143 -
all-1203 -
obs--98.45 %
Refinement TLS params.Method: refined / Origin x: 47.9946 Å / Origin y: 28.75 Å / Origin z: 35.2154 Å
111213212223313233
T-0.0554 Å2-0.0204 Å2-0.0126 Å2--0.0386 Å2-0.012 Å2---0.0479 Å2
L0.5587 °2-0.2025 °20.5506 °2-0.4577 °2-0.3822 °2--2.157 °2
S0.0121 Å °-0.0436 Å °0.0404 Å °0.0609 Å °0.0094 Å °-0.0766 Å °-0.1197 Å °0.0743 Å °-0.0215 Å °

+
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