[English] 日本語
Yorodumi
- PDB-3fw0: Structure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fw0
TitleStructure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase (PAL) bound to alpha-hydroxyhippuric acid (non-peptidic substrate)
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsLYASE / BETA PROPELLER / ZINC / CALCIUM / MERCURY / PEPTIDE AMIDATION / SUBSTRATE / HYDROXYHIPPURIC ACID / Alternative splicing / Cleavage on pair of basic residues / Copper / Cytoplasmic vesicle / Glycoprotein / Membrane / Metal-binding / Monooxygenase / Multifunctional enzyme / Oxidoreductase / Phosphoprotein / Sulfation / Transmembrane / Vitamin C
Function / homology
Function and homology information


peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process ...peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process / response to pH / mitotic chromosome condensation / L-ascorbic acid binding / response to copper ion / limb development / transport vesicle membrane / response to zinc ion / maternal process involved in female pregnancy / condensed chromosome / response to glucocorticoid / lactation / secretory granule / regulation of actin cytoskeleton organization / trans-Golgi network / response to estradiol / heart development / perikaryon / response to hypoxia / response to xenobiotic stimulus / copper ion binding / neuronal cell body / chromatin binding / calcium ion binding / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / cell surface / extracellular space / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. ...Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / NHL repeat profile. / NHL repeat / NHL repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
: / (2S)-hydroxy[(phenylcarbonyl)amino]ethanoic acid / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsChufan, E.E. / De, M. / Eipper, B.A. / Mains, R.E. / Amzel, L.M.
CitationJournal: Structure / Year: 2009
Title: Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme.
Authors: Chufan, E.E. / De, M. / Eipper, B.A. / Mains, R.E. / Amzel, L.M.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Peptidyl-glycine alpha-amidating monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5515
Polymers36,9141
Non-polymers6364
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.930, 75.080, 97.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Peptidyl-glycine alpha-amidating monooxygenase / PAM / Peptidylglycine alpha-hydroxylating monooxygenase / PHM / Peptidyl-alpha-hydroxyglycine alpha- ...PAM / Peptidylglycine alpha-hydroxylating monooxygenase / PHM / Peptidyl-alpha-hydroxyglycine alpha-amidating lyase / Peptidylamidoglycolate lyase / PAL


Mass: 36914.090 Da / Num. of mol.: 1
Fragment: Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase catalytic core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pam / Cell line (production host): Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14925, peptidylamidoglycolate lyase
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HH3 / (2S)-hydroxy[(phenylcarbonyl)amino]ethanoic acid / alpha-hydroxyhippuric acid


Mass: 195.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate pH=4.8, 0.5mM mercury(II) acetate - 0.2ml mother liquor in reservoir. Then, crystals soaked in 5mM hydroxyhippuric acid for several hours, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.00724 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 9, 2008 / Details: Monochromator Kohzu HLD-4 Double Crystal
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00724 Å / Relative weight: 1
ReflectionResolution: 2.5→59.34 Å / Num. all: 13347 / Num. obs: 13347 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rsym value: 0.075 / Net I/σ(I): 23.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1306 / Rsym value: 0.48 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PALcc native, being deposited at the same time as this structure

Resolution: 2.52→59.34 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.474 / SU ML: 0.216 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.689 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26019 655 4.9 %RANDOM
Rwork0.20672 ---
obs0.20939 12648 99.09 %-
all-13347 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.912 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2--0.24 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.52→59.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 17 118 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212721
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9263694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5525330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24724.317139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92515413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7851511
X-RAY DIFFRACTIONr_chiral_restr0.1150.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022155
X-RAY DIFFRACTIONr_nbd_refined0.1950.21170
X-RAY DIFFRACTIONr_nbtor_refined0.310.21762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.28
X-RAY DIFFRACTIONr_mcbond_it0.311.51676
X-RAY DIFFRACTIONr_mcangle_it0.54122664
X-RAY DIFFRACTIONr_scbond_it1.21331163
X-RAY DIFFRACTIONr_scangle_it1.2374.51030
LS refinement shellResolution: 2.515→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 48 -
Rwork0.274 846 -
obs-1306 92.64 %

+
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