[English] 日本語
Yorodumi
- PDB-1ibu: STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE AT 25 C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ibu
TitleSTRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE AT 25 C
Components
  • HISTIDINE DECARBOXYLASE ALPHA CHAIN
  • HISTIDINE DECARBOXYLASE BETA CHAIN
KeywordsLYASE / HELIX DISORDER / LESS ACTIVE FORM / SITE-DIRECTED MUTANT / PYRUVOYL / CARBOXY-LYASE
Function / homology
Function and homology information


histidine decarboxylase / histidine decarboxylase activity / L-histidine metabolic process
Similarity search - Function
Pyruvoyl-Dependent Histidine Decarboxylas; Chain A / Pyruvoyl-Dependent Histidine Decarboxylas, subunit A / Histidine decarboxylase proenzyme / Histidine decarboxylase proenzyme, N-terminal / Histidine carboxylase PI chain / Pyruvoyl-Dependent Histidine Decarboxylase, subunit B / Pyruvoyl-dependent histidine/arginine decarboxylase / Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich ...Pyruvoyl-Dependent Histidine Decarboxylas; Chain A / Pyruvoyl-Dependent Histidine Decarboxylas, subunit A / Histidine decarboxylase proenzyme / Histidine decarboxylase proenzyme, N-terminal / Histidine carboxylase PI chain / Pyruvoyl-Dependent Histidine Decarboxylase, subunit B / Pyruvoyl-dependent histidine/arginine decarboxylase / Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich / Few Secondary Structures / Irregular / Alpha Beta
Similarity search - Domain/homology
Histidine decarboxylase proenzyme
Similarity search - Component
Biological speciesLactobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWorley, S. / Schelp, E. / Monzingo, A.F. / Ernst, S. / Robertus, J.D.
CitationJournal: Proteins / Year: 2002
Title: Structure and cooperativity of a T-state mutant of histidine decarboxylase from Lactobacillus 30a.
Authors: Worley, S. / Schelp, E. / Monzingo, A.F. / Ernst, S. / Robertus, J.D.
History
DepositionMar 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HISTIDINE DECARBOXYLASE BETA CHAIN
B: HISTIDINE DECARBOXYLASE ALPHA CHAIN
C: HISTIDINE DECARBOXYLASE BETA CHAIN
D: HISTIDINE DECARBOXYLASE ALPHA CHAIN
E: HISTIDINE DECARBOXYLASE BETA CHAIN
F: HISTIDINE DECARBOXYLASE ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)102,4036
Polymers102,4036
Non-polymers00
Water00
1
A: HISTIDINE DECARBOXYLASE BETA CHAIN
B: HISTIDINE DECARBOXYLASE ALPHA CHAIN
C: HISTIDINE DECARBOXYLASE BETA CHAIN
D: HISTIDINE DECARBOXYLASE ALPHA CHAIN
E: HISTIDINE DECARBOXYLASE BETA CHAIN
F: HISTIDINE DECARBOXYLASE ALPHA CHAIN

A: HISTIDINE DECARBOXYLASE BETA CHAIN
B: HISTIDINE DECARBOXYLASE ALPHA CHAIN
C: HISTIDINE DECARBOXYLASE BETA CHAIN
D: HISTIDINE DECARBOXYLASE ALPHA CHAIN
E: HISTIDINE DECARBOXYLASE BETA CHAIN
F: HISTIDINE DECARBOXYLASE ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)204,80512
Polymers204,80512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25900 Å2
ΔGint-119 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.283, 119.037, 203.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a hexamer generated by applying a crystallographic two-fold to the trimer in the asymmetric unit: -x, y, -z + 1/2

-
Components

#1: Protein HISTIDINE DECARBOXYLASE BETA CHAIN / PI CHAIN


Mass: 8848.862 Da / Num. of mol.: 3 / Fragment: BETA CHAIN (RESIDUES 1-81) / Mutation: D53N, D54N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. (bacteria) / Strain: 30A / Gene: HDCA / Production host: Escherichia coli (E. coli) / References: UniProt: P00862, histidine decarboxylase
#2: Protein HISTIDINE DECARBOXYLASE ALPHA CHAIN


Mass: 25285.375 Da / Num. of mol.: 3 / Fragment: ALPHA CHAIN (RESIDUES 82-310)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. (bacteria) / Strain: 30A / Gene: HDCA / Production host: Escherichia coli (E. coli) / References: UniProt: P00862, histidine decarboxylase
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
20-15 %PEG4001reservoir
34-8 %PEG40001reservoir
40.1 Msodium acetate1reservoirpH4.6

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 18, 1996
RadiationMonochromator: DOUBLE FOCUSSING MIRRORS (NI & PT) + NI FILTER
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→10 Å / Num. all: 17480 / Num. obs: 17480 / % possible obs: 81.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.414 / % possible all: 88.6
Reflection
*PLUS
Lowest resolution: 10 Å / Redundancy: 3.3 %
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.6

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PYA

1pya


Resolution: 3.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.3296 832 RANDOM
Rwork0.27 --
obs0.273 17143 -
all-17467 -
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 0 0 6856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg3.42
Refinement
*PLUS
σ(F): 2 / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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