[English] 日本語
Yorodumi
- PDB-6mpz: Crystal structure of a double glycine motif protease from AMS/PCA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mpz
TitleCrystal structure of a double glycine motif protease from AMS/PCAT transporter in complex with the leader peptide
Components
  • Double Glycine Motif Protease domain from AMS/PCAT Transporter
  • peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide
KeywordsTRANSPORT PROTEIN / peptide secretion / peptidase C39 domain / leader peptide / lantibiotic
Function / homology3,6,9,12,15,18-HEXAOXAICOSANE
Function and homology information
Biological speciesLachnospiraceae bacterium C6A11 (bacteria)
Prochlorococcus marinus str. MIT 9313 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsDong, S.-H. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079038 United States
CitationJournal: Elife / Year: 2019
Title: Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease.
Authors: Bobeica, S.C. / Dong, S. / Huo, L. / Mazo, N. / McLaughlin, M.I.H. / Jimenez-Oses, G. / Nair, S.K. / van der Donk, W.A.
History
DepositionOct 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Double Glycine Motif Protease domain from AMS/PCAT Transporter
B: Double Glycine Motif Protease domain from AMS/PCAT Transporter
C: Double Glycine Motif Protease domain from AMS/PCAT Transporter
D: Double Glycine Motif Protease domain from AMS/PCAT Transporter
M: peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide
N: peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide
O: peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide
P: peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,86510
Polymers72,2768
Non-polymers5892
Water2,216123
1
A: Double Glycine Motif Protease domain from AMS/PCAT Transporter
M: peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3633
Polymers18,0692
Non-polymers2941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-8 kcal/mol
Surface area7910 Å2
MethodPISA
2
B: Double Glycine Motif Protease domain from AMS/PCAT Transporter
N: peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3633
Polymers18,0692
Non-polymers2941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area7680 Å2
MethodPISA
3
C: Double Glycine Motif Protease domain from AMS/PCAT Transporter
O: peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide


Theoretical massNumber of molelcules
Total (without water)18,0692
Polymers18,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-5 kcal/mol
Surface area7600 Å2
MethodPISA
4
D: Double Glycine Motif Protease domain from AMS/PCAT Transporter
P: peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide


Theoretical massNumber of molelcules
Total (without water)18,0692
Polymers18,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-5 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.888, 119.426, 76.522
Angle α, β, γ (deg.)90.00, 93.84, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17M
27N
18M
28O
19M
29P
110N
210O
111N
211P
112O
212P

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
11GLNGLNPROPROAA5 - 1435 - 143
21GLNGLNPROPROBB5 - 1435 - 143
12GLNGLNPROPROAA5 - 1435 - 143
22GLNGLNPROPROCC5 - 1435 - 143
13GLNGLNTHRTHRAA5 - 1445 - 144
23GLNGLNTHRTHRDD5 - 1445 - 144
14GLNGLNTHRTHRBB5 - 1445 - 144
24GLNGLNTHRTHRCC5 - 1445 - 144
15GLNGLNPROPROBB5 - 1435 - 143
25GLNGLNPROPRODD5 - 1435 - 143
16GLNGLNPROPROCC5 - 1435 - 143
26GLNGLNPROPRODD5 - 1435 - 143
17GLYGLYGLYGLYME1 - 131 - 13
27GLYGLYGLYGLYNF1 - 131 - 13
18GLYGLYGLYGLYME1 - 131 - 13
28GLYGLYGLYGLYOG1 - 131 - 13
19GLYGLYGLYGLYME1 - 131 - 13
29GLYGLYGLYGLYPH1 - 131 - 13
110GLYGLYGLYGLYNF1 - 131 - 13
210GLYGLYGLYGLYOG1 - 131 - 13
111GLYGLYGLYGLYNF1 - 131 - 13
211GLYGLYGLYGLYPH1 - 131 - 13
112GLYGLYGLYGLYOG1 - 131 - 13
212GLYGLYGLYGLYPH1 - 131 - 13

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

-
Components

#1: Protein
Double Glycine Motif Protease domain from AMS/PCAT Transporter


Mass: 16752.646 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium C6A11 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Protein/peptide
peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptide


Mass: 1316.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus str. MIT 9313 (bacteria)
Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-16P / 3,6,9,12,15,18-HEXAOXAICOSANE


Mass: 294.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 282 K / Method: vapor diffusion / pH: 8.5
Details: 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.0 2M N-acetyl-D-glucosamine, 0.05 M Tris and BICINE pH 8.5, 20% v/v polyethylene glycol 500 ...Details: 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.0 2M N-acetyl-D-glucosamine, 0.05 M Tris and BICINE pH 8.5, 20% v/v polyethylene glycol 500 monomethyl ether, 10% w/v polyethylene glycol 20000, and 8% v/v formamide
Temp details: 9 Celsius

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.98→76.4 Å / Num. obs: 47187 / % possible obs: 99.8 % / Redundancy: 5.1 % / Net I/σ(I): 9.3
Reflection shellResolution: 1.98→1.985 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata scaling
AutoSolphasing
PHENIXmodel building
RefinementResolution: 2→50.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.264 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26829 2306 5 %RANDOM
Rwork0.23434 ---
obs0.23606 43389 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.026 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å2-0 Å20.47 Å2
2---4.37 Å2-0 Å2
3---6.4 Å2
Refinement stepCycle: 1 / Resolution: 2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4843 0 44 123 5010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194993
X-RAY DIFFRACTIONr_bond_other_d0.0020.024785
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9736688
X-RAY DIFFRACTIONr_angle_other_deg1.0333.00111100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6125607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87524.064219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86415873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5811529
X-RAY DIFFRACTIONr_chiral_restr0.1040.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215450
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021019
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_it2.993.4592468
X-RAY DIFFRACTIONr_mcbond_other2.9893.4592469
X-RAY DIFFRACTIONr_mcangle_it4.3925.1663059
X-RAY DIFFRACTIONr_mcangle_other4.3915.1663060
X-RAY DIFFRACTIONr_scbond_it3.543.9112525
X-RAY DIFFRACTIONr_scbond_other3.5393.9112526
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3925.6923630
X-RAY DIFFRACTIONr_long_range_B_refined7.41439.5045183
X-RAY DIFFRACTIONr_long_range_B_other7.41439.4885174
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)
11A87060.06
12B87060.06
21A86980.06
22C86980.06
31A86760.06
32D86760.06
41B87580.06
42C87580.06
51B86560.05
52D86560.05
61C86520.06
62D86520.06
71M5460.01
72N5460.01
81M5440.02
82O5440.02
91M5460.01
92P5460.01
101N5480.02
102O5480.02
111N5520.01
112P5520.01
121O5480.02
122P5480.02
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 172 -
Rwork0.392 3171 -
obs--99.97 %

+
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