[English] 日本語
Yorodumi
- PDB-1ltu: CRYSTAL STRUCTURE OF CHROMOBACTERIUM VIOLACEUM, APO (NO IRON BOUN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ltu
TitleCRYSTAL STRUCTURE OF CHROMOBACTERIUM VIOLACEUM, APO (NO IRON BOUND) STRUCTURE
ComponentsPHENYLALANINE-4-HYDROXYLASE
KeywordsOXIDOREDUCTASE / PHENYLALANINE HYDROXYLASE APO-STRUCTURE
Function / homology
Function and homology information


phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / L-phenylalanine catabolic process / iron ion binding
Similarity search - Function
Phenylalanine-4-hydroxylase, monomeric form / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase superfamily / Biopterin-dependent aromatic amino acid hydroxylase ...Phenylalanine-4-hydroxylase, monomeric form / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase superfamily / Biopterin-dependent aromatic amino acid hydroxylase / Biopterin-dependent aromatic amino acid hydroxylase family profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsErlandsen, H. / Kim, J.Y. / Patch, M.G. / Han, A. / Volner, A. / Abu-Omar, M.M. / Stevens, R.C.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural comparison of bacterial and human iron-dependent phenylalanine hydroxylases: similar fold, different stability and reaction rates.
Authors: Erlandsen, H. / Kim, J.Y. / Patch, M.G. / Han, A. / Volner, A. / Abu-Omar, M.M. / Stevens, R.C.
History
DepositionMay 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHENYLALANINE-4-HYDROXYLASE


Theoretical massNumber of molelcules
Total (without water)33,6281
Polymers33,6281
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.684, 68.011, 90.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PHENYLALANINE-4-HYDROXYLASE / PAH / Phe-4-monooxygenase / Phenylalaninase


Mass: 33627.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P30967, phenylalanine 4-monooxygenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, NaCl, HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.65-1.90 Mammonium sulfate1reservoir
240-100 mM1reservoirNaCl
320 mMHEPES1reservoirpH7.5
420 mg/mlprotein1drop

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.919866,0.91961,0.942813
20.785
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monomchromatorMADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9198661
20.919611
30.9428131
40.7851
ReflectionResolution: 1.74→18.5 Å / Num. all: 30448 / Num. obs: 30448 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.4
Reflection shellResolution: 1.74→1.76 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1490 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 1.73 Å / Lowest resolution: 20 Å / Redundancy: 5-6 / Num. measured all: 124221 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 1.73 Å / % possible obs: 99.7 % / Redundancy: 5-6 / Rmerge(I) obs: 0.566

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.74→18.5 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4709 -Random
Rwork0.197 ---
all-28930 --
obs-28930 94 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---1.63 Å20 Å2
3---2.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.74→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 0 198 2472
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.46
Refinement
*PLUS
Highest resolution: 1.73 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.46
LS refinement shell
*PLUS
Highest resolution: 1.73 Å / Lowest resolution: 1.76 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://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