[English] 日本語
Yorodumi
- PDB-2j56: X-ray reduced Paraccocus denitrificans methylamine dehydrogenase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j56
TitleX-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- semiquinone in complex with amicyanin.
Components
  • (METHYLAMINE DEHYDROGENASE ...) x 2
  • AMICYANIN
KeywordsOXIDOREDUCTASE / PERIPLASMIC / METAL-BINDING / ELECTRON TRANSPORT / SINGLE CRYSTAL MICROSPECTROPHOTOMETRY
Function / homology
Function and homology information


methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Amicyanin, Paracoccus/Methylobacterium / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) ...Amicyanin, Paracoccus/Methylobacterium / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain / Amicyanin/Pseudoazurin / Quinoprotein amine dehydrogenase, beta chain-like / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cupredoxins - blue copper proteins / Cupredoxin / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesPARACOCCUS DENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsPearson, A.R. / Pahl, R. / Davidson, V.L. / Wilmot, C.M.
Citation
Journal: J.Synchrotron Radiat. / Year: 2007
Title: Tracking X-Ray-Derived Redox Changes in Crystals of a Methylamine Dehydrogenase/Amicyanin Complex Using Single-Crystal Uv/Vis Microspectrophotometry.
Authors: Pearson, A.R. / Pahl, R. / Kovaleva, E.G. / Davidson, V.L. / Wilmot, C.M.
#1: Journal: To be Published
Title: Crystallographic Structures of Methylamine Dehydrogenase Catalytic Intermediates from Paraccocus Denitrificans
Authors: De La Mora-Rey, T. / Pearson, A.R. / Hoeffner, E. / Watts, K.T. / Yucel, N. / Davidson, V.L. / Wilmot, C.M.
History
DepositionSep 12, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AMICYANIN
B: AMICYANIN
H: METHYLAMINE DEHYDROGENASE HEAVY CHAIN
J: METHYLAMINE DEHYDROGENASE HEAVY CHAIN
L: METHYLAMINE DEHYDROGENASE LIGHT CHAIN
M: METHYLAMINE DEHYDROGENASE LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,59311
Polymers136,3286
Non-polymers2655
Water18,6091033
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17050 Å2
ΔGint-92.4 kcal/mol
Surface area41600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.029, 123.029, 245.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein / METHYLAMINE DEHYDROGENASE ... / Antibody , 3 types, 6 molecules ABHJLM

#1: Protein AMICYANIN


Mass: 11505.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: AMICYANIN IS THE OBLIGATE ELECTRON TRANSFER PARTNER OF METHYLAMINE DEHYDROGENASE.
Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / References: UniProt: P22364
#2: Protein METHYLAMINE DEHYDROGENASE HEAVY CHAIN / METHYLAMINE DEHYDROGENASE ALPHA CHAIN / MADH


Mass: 42449.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / References: UniProt: P29894, EC: 1.4.99.3
#3: Antibody METHYLAMINE DEHYDROGENASE LIGHT CHAIN / METHYLAMINE DEHYDROGENASE BETA CHAIN / MADH


Mass: 14209.712 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / References: UniProt: P22619, EC: 1.4.99.3

-
Non-polymers , 4 types, 1038 molecules

#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1033 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsAT PRESENT, THE SEQUENCE DATABASES INDICATE THAT RESIDUE 312 OF THE HEAVY CHAIN IS LEU AND RESIDUE ...AT PRESENT, THE SEQUENCE DATABASES INDICATE THAT RESIDUE 312 OF THE HEAVY CHAIN IS LEU AND RESIDUE 313 IS LEU. THE AUTHORS WHO DEPOSITED 2MTA FOUND THAT THEY MISREAD THE GELS AND THAT RESIDUES 312 AND 313 SHOULD BE PHE AND VAL, RESPECTIVELY. IN THIS ENTRY THE SEQUENCE ERRORS HAVE BEEN CORRECTED.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.92 %
Crystal growpH: 9 / Details: pH 9.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→43.5 Å / Num. obs: 101798 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 22
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 7.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.1→43.48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.525 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5353 5 %RANDOM
Rwork0.169 ---
obs0.171 101798 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9342 0 10 1033 10385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229628
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.95313144
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.95451207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08624.041443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.814151443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7131556
X-RAY DIFFRACTIONr_chiral_restr0.1150.21423
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027542
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.24615
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.26499
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.21092
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8491.56042
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47429746
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.41133735
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8364.53397
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 415
Rwork0.206 7492

+
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://pdbjlvh1.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