[English] 日本語
Yorodumi
- PDB-4zur: Crystal structure of acetylpolyamine amidohydrolase from Mycoplan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zur
TitleCrystal structure of acetylpolyamine amidohydrolase from Mycoplana ramosa in complex with a hydroxamate inhibitor
ComponentsAcetylpolyamine aminohydrolase
KeywordsHydrolase/Hydrolase inhibitor / acetylpolyamine amidohydrolase / arginase fold / enzyme-inhibitor complex / polyamine / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / epigenetic regulation of gene expression / metal ion binding
Similarity search - Function
Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-amino-N-hydroxyheptanamide / : / AMMONIUM ION / Acetylpolyamine amidohydrolase
Similarity search - Component
Biological speciesMycoplana ramosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsDecroos, C. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Biochemistry / Year: 2015
Title: Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase.
Authors: Decroos, C. / Christianson, D.W.
History
DepositionMay 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetylpolyamine aminohydrolase
B: Acetylpolyamine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,58213
Polymers72,7402
Non-polymers84211
Water18,9701053
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-21 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.990, 120.700, 64.520
Angle α, β, γ (deg.)90.00, 97.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Acetylpolyamine aminohydrolase


Mass: 36369.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplana ramosa (bacteria) / Gene: aphA, aph / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q48935

-
Non-polymers , 6 types, 1064 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-7XA / 7-amino-N-hydroxyheptanamide


Mass: 160.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1053 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M NH4Cl, 20% (w/v) PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.13→22.8 Å / Num. obs: 248014 / % possible obs: 98.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.8
Reflection shellResolution: 1.13→1.19 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 3.9 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
PHENIXDEV_1833refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q9B

3q9b


Resolution: 1.13→22.8 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.136 12379 4.99 %
Rwork0.114 --
obs0.115 247921 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.13→22.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5127 0 46 1053 6226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015690
X-RAY DIFFRACTIONf_angle_d1.4347774
X-RAY DIFFRACTIONf_dihedral_angle_d12.452029
X-RAY DIFFRACTIONf_chiral_restr0.088822
X-RAY DIFFRACTIONf_plane_restr0.0091046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.132-1.14490.22533920.19347578X-RAY DIFFRACTION95
1.1449-1.15830.19223920.18247734X-RAY DIFFRACTION96
1.1583-1.17250.19983970.1697677X-RAY DIFFRACTION96
1.1725-1.18730.1944120.1577726X-RAY DIFFRACTION97
1.1873-1.20290.17584220.14547675X-RAY DIFFRACTION97
1.2029-1.21940.16833920.14027787X-RAY DIFFRACTION97
1.2194-1.23680.16684100.13497725X-RAY DIFFRACTION97
1.2368-1.25530.1524300.12737775X-RAY DIFFRACTION97
1.2553-1.27490.1494160.12467829X-RAY DIFFRACTION98
1.2749-1.29580.1434480.12057718X-RAY DIFFRACTION97
1.2958-1.31810.13993700.11587857X-RAY DIFFRACTION98
1.3181-1.34210.14024150.11227811X-RAY DIFFRACTION98
1.3421-1.36790.14673970.11117820X-RAY DIFFRACTION98
1.3679-1.39580.1363900.10897810X-RAY DIFFRACTION98
1.3958-1.42620.14244240.10447855X-RAY DIFFRACTION98
1.4262-1.45930.1283700.10267907X-RAY DIFFRACTION98
1.4593-1.49580.12754150.1017844X-RAY DIFFRACTION98
1.4958-1.53630.12374110.09387873X-RAY DIFFRACTION98
1.5363-1.58150.12184350.09177841X-RAY DIFFRACTION99
1.5815-1.63250.11814490.09287900X-RAY DIFFRACTION99
1.6325-1.69080.11374430.09277941X-RAY DIFFRACTION99
1.6908-1.75850.11383770.09558016X-RAY DIFFRACTION100
1.7585-1.83850.11984330.10027999X-RAY DIFFRACTION100
1.8385-1.93540.12034210.10928004X-RAY DIFFRACTION100
1.9354-2.05660.13474160.11418037X-RAY DIFFRACTION100
2.0566-2.21520.12394000.10988037X-RAY DIFFRACTION100
2.2152-2.43790.11894210.10778009X-RAY DIFFRACTION100
2.4379-2.79020.13114800.10978007X-RAY DIFFRACTION100
2.7902-3.51320.13733970.11698043X-RAY DIFFRACTION100
3.5132-22.80770.13614040.11937707X-RAY DIFFRACTION95

+
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