[English] 日本語
Yorodumi
- PDB-6h1b: Structure of amide bond synthetase Mcba K483A mutant from Marinac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h1b
TitleStructure of amide bond synthetase Mcba K483A mutant from Marinactinospora thermotolerans
ComponentsFatty acid CoA ligase
KeywordsLIGASE / McbA / amide / ATP / ANL enzyme
Function / homology
Function and homology information


ligase activity, forming carbon-sulfur bonds / nucleotide binding
Similarity search - Function
: / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 ...: / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Chem-EQ2 / Fatty acid CoA ligase
Similarity search - Component
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRowlinson, B. / Petchey, M. / Cuetos, A. / Frese, A. / Dannevald, S. / Grogan, G.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: The Broad Aryl Acid Specificity of the Amide Bond Synthetase McbA Suggests Potential for the Biocatalytic Synthesis of Amides.
Authors: Petchey, M. / Cuetos, A. / Rowlinson, B. / Dannevald, S. / Frese, A. / Sutton, P.W. / Lovelock, S. / Lloyd, R.C. / Fairlamb, I.J.S. / Grogan, G.
History
DepositionJul 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_PDB_obs_spr / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 8, 2023Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid CoA ligase
B: Fatty acid CoA ligase
C: Fatty acid CoA ligase
D: Fatty acid CoA ligase
E: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,09915
Polymers266,0915
Non-polymers3,00710
Water3,495194
1
A: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Fatty acid CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,2181
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.234, 130.738, 196.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHRAA-1 - 4943 - 498
21PROPROTHRTHRBB-1 - 4943 - 498
12PROPROTHRTHRAA-1 - 4943 - 498
22PROPROTHRTHRCC-1 - 4943 - 498
13PROPROTHRTHRAA-1 - 4943 - 498
23PROPROTHRTHRDD-1 - 4943 - 498
14METMETTHRTHRAA1 - 4945 - 498
24METMETTHRTHREE1 - 4945 - 498
15PROPROTHRTHRBB-1 - 4943 - 498
25PROPROTHRTHRCC-1 - 4943 - 498
16PROPROTHRTHRBB-1 - 4943 - 498
26PROPROTHRTHRDD-1 - 4943 - 498
17METMETTHRTHRBB1 - 4945 - 498
27METMETTHRTHREE1 - 4945 - 498
18PROPROTHRTHRCC-1 - 4943 - 498
28PROPROTHRTHRDD-1 - 4943 - 498
19METMETASPASPCC1 - 4955 - 499
29METMETASPASPEE1 - 4955 - 499
110METMETTHRTHRDD1 - 4945 - 498
210METMETTHRTHREE1 - 4945 - 498

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

-
Components

#1: Protein
Fatty acid CoA ligase


Mass: 53218.293 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinactinospora thermotolerans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: R4R1U5
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-EQ2 / 1-ethanoyl-9~{H}-pyrido[3,4-b]indole-3-carboxylic acid


Mass: 254.241 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C14H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1. 6 M sodium citrate

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.8→108.83 Å / Num. obs: 75674 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.11 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.86 Å / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.67 / Rpim(I) all: 0.46

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GXQ

4gxq


Resolution: 2.8→101.5 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.899 / SU B: 16.689 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24775 3618 4.8 %RANDOM
Rwork0.20396 ---
obs0.20605 71980 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.194 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å2-0 Å2-0 Å2
2--1.97 Å2-0 Å2
3----4.66 Å2
Refinement stepCycle: 1 / Resolution: 2.8→101.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17686 0 206 196 18088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01418329
X-RAY DIFFRACTIONr_bond_other_d0.0020.01716365
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.66125137
X-RAY DIFFRACTIONr_angle_other_deg0.8791.6337975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg752422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35419.658819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.645152487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3315158
X-RAY DIFFRACTIONr_chiral_restr0.0630.22458
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023280
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4125.1579730
X-RAY DIFFRACTIONr_mcbond_other4.4125.1579729
X-RAY DIFFRACTIONr_mcangle_it6.7987.72712132
X-RAY DIFFRACTIONr_mcangle_other6.7977.72812133
X-RAY DIFFRACTIONr_scbond_it4.4795.3198599
X-RAY DIFFRACTIONr_scbond_other4.4795.3198600
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8577.87713004
X-RAY DIFFRACTIONr_long_range_B_refined9.79260.48119286
X-RAY DIFFRACTIONr_long_range_B_other9.79260.4819287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A143180.06
12B143180.06
21A143730.06
22C143730.06
31A144770.06
32D144770.06
41A137060.09
42E137060.09
51B142910.06
52C142910.06
61B143660.05
62D143660.05
71B135830.09
72E135830.09
81C143470.06
82D143470.06
91C135970.09
92E135970.09
101D136150.09
102E136150.09
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 282 -
Rwork0.327 5258 -
obs--100 %

+
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