[English] 日本語
Yorodumi
- PDB-4mi4: Crystal structure of spermidine N-acetyltransferase from Vibrio c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mi4
TitleCrystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with spermine
ComponentsSpermidine n1-acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / spermidine / N-acetyltransferase
Function / homology
Function and homology information


polyamine catabolic process / spermine catabolic process / spermidine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / magnesium ion binding / cytoplasm
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
SPERMINE / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Kuhn, M.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Mol.Biol. / Year: 2015
Title: A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure.
Authors: Filippova, E.V. / Kuhn, M.L. / Osipiuk, J. / Kiryukhina, O. / Joachimiak, A. / Ballicora, M.A. / Anderson, W.F.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Atomic model
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9496
Polymers70,3423
Non-polymers6073
Water9,854547
1
A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,79624
Polymers281,36812
Non-polymers2,42812
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area40400 Å2
ΔGint25 kcal/mol
Surface area81450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.633, 135.898, 140.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Spermidine n1-acetyltransferase


Mass: 23447.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El tor (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9KL03
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris HCl, 20% Ethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2011 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987856 Å / Relative weight: 1
ReflectionResolution: 1.848→30 Å / Num. all: 59130 / Num. obs: 59130 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 38.8
Reflection shellResolution: 1.848→1.88 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 6.6 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EG7

3eg7
PDB Unreleased entry


Resolution: 1.848→28.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.097 / SU ML: 0.065 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2975 5.1 %RANDOM
Rwork0.14936 ---
obs0.15115 55591 99.23 %-
all-55591 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.563 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---1.08 Å2-0 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.848→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 42 547 4889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194549
X-RAY DIFFRACTIONr_bond_other_d0.0010.024317
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.946141
X-RAY DIFFRACTIONr_angle_other_deg0.89539861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2675525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94523.81273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.17715793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3581538
X-RAY DIFFRACTIONr_chiral_restr0.1360.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025267
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021221
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6152.0482079
X-RAY DIFFRACTIONr_mcbond_other2.6152.0482078
X-RAY DIFFRACTIONr_mcangle_it3.3423.0512611
X-RAY DIFFRACTIONr_mcangle_other3.3413.0512612
X-RAY DIFFRACTIONr_scbond_it4.1532.4262470
X-RAY DIFFRACTIONr_scbond_other4.1522.4272471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7293.5013531
X-RAY DIFFRACTIONr_long_range_B_refined7.79618.5815590
X-RAY DIFFRACTIONr_long_range_B_other7.62917.5865309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 215 -
Rwork0.175 3829 -
obs--93.01 %
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)
10.16190.0540.05461.56790.1261.6025-0.0451-0.0143-0.0164-0.0540.0803-0.12910.0115-0.0187-0.03520.02720.0049-0.00610.0559-0.02860.064220.5051-53.3998-24.612
20.2775-0.2546-0.04530.24820.14481.04150.0101-0.04320.04020.00570.0489-0.04920.02360.0726-0.05890.0385-0.0031-0.01150.0315-0.00060.081815.0362-57.0552-25.8981
30.42910.01730.07130.54040.08430.1865-0.0250.0122-0.0216-0.11130.0532-0.1091-0.009-0.0292-0.02820.0492-0.01670.03280.031-0.00020.088313.5625-53.4036-40.2783
40.10140.16850.12791.0613-0.29190.5717-0.0665-0.0014-0.0121-0.2630.0494-0.0184-0.03890.05740.01710.0917-0.03010.01320.0880.00760.08467.041-46.5818-38.4048
50.1509-0.1046-0.21560.5831-0.18970.8623-0.01080.0303-0.03030.0067-0.0269-0.0266-0.0543-0.12310.03770.0522-0.00290.00010.0902-0.03030.0458-16.6344-42.8182-0.197
63.18340.0421-0.77450.56360.55930.80.00650.26870.0257-0.0199-0.08180.0615-0.0663-0.18420.07530.06220.0331-0.02350.09360.00880.0664-18.185-33.666.5844
70.19250.1182-0.3440.2493-0.09991.58050.02370.0188-0.02020.0108-0.00390.035-0.1595-0.1871-0.01980.05610.035-0.0190.04780.00560.0652-9.9155-25.33193.1479
80.5655-0.1053-0.27191.94040.75620.39940.16610.04030.0439-0.0764-0.17460.1467-0.1463-0.07530.00850.23540.03190.0070.0364-0.0060.0848-7.4387-23.34814.9503
90.16940.10050.04911.35430.45210.8428-0.036-0.0103-0.01820.0378-0.02590.16640.0066-0.0030.06180.04230.0010.03130.0137-0.00920.0917-16.4329-55.7592-21.7056
102.0449-0.4720.02031.5974-0.09310.079-0.00380.0465-0.1653-0.0006-0.02830.3235-0.0363-0.04650.03210.03370.0072-0.01270.0979-0.02810.1205-18.2531-45.1661-26.2399
110.1321-0.2339-0.08551.05780.29880.22520.0134-0.0185-0.0344-0.0979-0.05670.1013-0.0368-0.07530.04340.04270.0046-0.02340.0684-0.00690.0712-9.1242-44.5118-35.9527
124.2056-6.98520.624115.4444-3.11571.218-0.12150.026-0.0670.05350.12940.13190.0651-0.0859-0.0080.09540.0321-0.0280.0289-0.00030.0857-10.3435-27.1031-30.5488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 33
2X-RAY DIFFRACTION2A34 - 96
3X-RAY DIFFRACTION3A97 - 141
4X-RAY DIFFRACTION4A142 - 171
5X-RAY DIFFRACTION5B3 - 59
6X-RAY DIFFRACTION6B60 - 105
7X-RAY DIFFRACTION7B106 - 153
8X-RAY DIFFRACTION8B154 - 170
9X-RAY DIFFRACTION9C4 - 59
10X-RAY DIFFRACTION10C60 - 105
11X-RAY DIFFRACTION11C106 - 165
12X-RAY DIFFRACTION12C166 - 173

+
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