[English] 日本語
Yorodumi
- PDB-4q3c: PylD cocrystallized with L-Lysine-Ne-L-lysine and NAD+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q3c
TitlePylD cocrystallized with L-Lysine-Ne-L-lysine and NAD+
ComponentsPylD, pyrrolysine synthase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / Pyrrolysine
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Rossmann fold - #12150 / Pyrrolysine biosynthesis protein PylD / : / Pyrrolysine biosynthesis protein PylD, N-terminal domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N~6~-L-lysyl-L-lysine / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Pyrrolysine biosynthesis protein PylD N-terminal domain-containing protein
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsQuitterer, F. / Beck, P. / Bacher, A. / Groll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).
Authors: Quitterer, F. / Beck, P. / Bacher, A. / Groll, M.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Structure summary
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Aug 20, 2014Group: Database references
Revision 1.4Sep 20, 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 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _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: PylD, pyrrolysine synthase
B: PylD, pyrrolysine synthase
C: PylD, pyrrolysine synthase
D: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,45628
Polymers111,8554
Non-polymers4,60124
Water4,918273
1
A: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,41111
Polymers27,9641
Non-polymers1,44810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1477
Polymers27,9641
Non-polymers1,1836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9495
Polymers27,9641
Non-polymers9854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9495
Polymers27,9641
Non-polymers9854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: PylD, pyrrolysine synthase
hetero molecules

B: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,55918
Polymers55,9282
Non-polymers2,63116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area6290 Å2
ΔGint-67 kcal/mol
Surface area21000 Å2
MethodPISA
6
C: PylD, pyrrolysine synthase
hetero molecules

D: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,89810
Polymers55,9282
Non-polymers1,9708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area4690 Å2
ΔGint-75 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.250, 259.770, 48.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.986375, 0.164432, 0.005198), (-0.16444, -0.986386, -0.001306), (0.004912, -0.002143, 0.999986)0.90798, 133.52715, 15.91163
3given(-0.544518, -0.034984, 0.838019), (0.028481, 0.997782, 0.06016), (-0.838266, 0.056626, -0.542314)13.58919, -62.36528, 23.3923
4given(0.531105, 0.159981, 0.832066), (0.10026, -0.98698, 0.12577), (0.841353, 0.016626, -0.54023)-17.9229, 67.60268, 22.16523

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
PylD, pyrrolysine synthase


Mass: 27963.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina barkeri (archaea) / Strain: Fusaro / Gene: Mbar_A0835 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q46E80, Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor

-
Non-polymers , 8 types, 297 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-2YG / N~6~-L-lysyl-L-lysine


Type: L-peptide linking / Mass: 274.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26N4O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS; 27% PEG3350; 0.2 M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 66293 / Num. obs: 66181 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4Q39

4q39


Resolution: 2.1→15 Å / SU B: 9.944 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19796 3260 4.9 %RANDOM
Rwork0.16899 ---
obs0.17044 62849 99.85 %-
all-66109 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.106 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0 Å2
2---1.35 Å20 Å2
3---3.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7816 0 295 273 8384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198253
X-RAY DIFFRACTIONr_bond_other_d0.0020.027843
X-RAY DIFFRACTIONr_angle_refined_deg1.512.01611221
X-RAY DIFFRACTIONr_angle_other_deg0.799318113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8751031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35825.802324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.163151321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3121520
X-RAY DIFFRACTIONr_chiral_restr0.0790.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021738
X-RAY DIFFRACTIONr_rigid_bond_restr2.563316092
X-RAY DIFFRACTIONr_sphericity_free37.4745102
X-RAY DIFFRACTIONr_sphericity_bonded26.829516125
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 218 -
Rwork0.253 4493 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01790.0242-0.00940.03790.00220.05310.0018-0.00830.00110.0075-0.00180.00170.00540.020400.06130.0032-00.0867-0.0010.00052.54551.47523.351
20.0031-0.00080.01110.0038-0.01540.0849-0.0017-0.0060.00280.00040.00130.0015-0.0115-0.02840.00040.06190.00020.00230.0868-0.00150.005112.0281.2637.495
30.1746-0.0044-0.0720.18070.0310.12380.01690.00780.0346-0.0031-0.01210.0179-0.0293-0.0228-0.00480.08170.0008-0.0050.1134-0.00090.00989.368113.916-2.423
40.15590.11630.14520.22110.04470.16790.06460.0395-0.03270.0405-0.0401-0.02230.07060.0702-0.02440.0755-0.01940.00450.1363-0.00490.018910.20919.20814.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 259
2X-RAY DIFFRACTION1A901 - 910
3X-RAY DIFFRACTION1A1001 - 1133
4X-RAY DIFFRACTION2B1 - 259
5X-RAY DIFFRACTION2B901 - 906
6X-RAY DIFFRACTION2B1001 - 1111
7X-RAY DIFFRACTION3C1 - 259
8X-RAY DIFFRACTION3C901 - 904
9X-RAY DIFFRACTION3C1001 - 1016
10X-RAY DIFFRACTION4D2 - 259
11X-RAY DIFFRACTION4D901 - 904
12X-RAY DIFFRACTION4D1001 - 1013

+
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