[English] 日本語
Yorodumi
- PDB-3gb0: Crystal structure of aminopeptidase PepT (NP_980509.1) from Bacil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gb0
TitleCrystal structure of aminopeptidase PepT (NP_980509.1) from Bacillus cereus ATCC 10987 at 2.04 A resolution
ComponentsPeptidase TTripeptide aminopeptidase
KeywordsHYDROLASE / NP_980509.1 / aminopeptidase PepT / Peptidase family M20/M25/M40 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Aminopeptidase / Metal-binding
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M20B, peptidase T-like / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Peptidase M42 / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 ...Peptidase M20B, peptidase T-like / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Peptidase M42 / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peptidase T
Similarity search - Component
Biological speciesBacillus cereus ATCC 10987 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.04 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of aminopeptidase PepT (NP_980509.1) from Bacillus cereus ATCC 10987 at 2.04 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _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: Peptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8388
Polymers40,1511
Non-polymers6877
Water3,855214
1
A: Peptidase T
hetero molecules

A: Peptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,67616
Polymers80,3022
Non-polymers1,37314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2880 Å2
ΔGint-8.5 kcal/mol
Surface area27910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.311, 58.147, 51.368
Angle α, β, γ (deg.)90.000, 91.750, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THAT A DIMER IS THE STABLE OLIGOMERIC FORM IN SOLUTION.

-
Components

#1: Protein Peptidase T / Tripeptide aminopeptidase


Mass: 40151.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 10987 (bacteria) / Gene: BCE_4216, NP_980509.1, pepT / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q731F0, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: NANODROP, 10.0% Glycerol, 5.0% PEG 1000, 30.0% PEG 600, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97959
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979591
ReflectionResolution: 2.04→29.463 Å / Num. obs: 26596 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.025 Å2 / Rmerge(I) obs: 0.07
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.04-2.110.5561.793074867196.2
2.11-2.20.3932.2103805396198.4
2.2-2.30.3052.898405109198.4
2.3-2.420.2513.397735066198.8
2.42-2.570.1954.399295125198.8
2.57-2.770.145.8100265174198.7
2.77-3.040.0918.697244995198.8
3.04-3.480.05114.3100455162198.6
3.48-4.380.02924.4100695139198.4
4.38-29.4630.0233.2100795141197.5

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.04→29.463 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.698 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.153
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GLYCEROL (GOL) AND POLYETHYLENE GLYCOL (PEG) FRAGMENTS FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. RESIDUES ASP107-ASP108 FORM A CIS-PEPTIDE WHICH IS SUPPORTED BY ELECTRON DENSITY. THIS IS IN THE PUTATIVE ACTIVE SITE AND MAY BE FUNCTIONALLY RELEVANT INDICATING THE POSSIBILITY OF CARBOHYDRATE BINDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1340 5 %RANDOM
Rwork0.169 ---
obs0.171 26590 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.86 Å2 / Biso mean: 26.603 Å2 / Biso min: 12.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å2-1.28 Å2
2--2.59 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.04→29.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 45 214 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222866
X-RAY DIFFRACTIONr_bond_other_d0.0010.021887
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9683872
X-RAY DIFFRACTIONr_angle_other_deg0.95734659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0465380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44225.652115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.34415486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7571511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
X-RAY DIFFRACTIONr_mcbond_it1.76531854
X-RAY DIFFRACTIONr_mcbond_other0.5133776
X-RAY DIFFRACTIONr_mcangle_it2.77452990
X-RAY DIFFRACTIONr_scbond_it5.53181012
X-RAY DIFFRACTIONr_scangle_it7.88211879
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 97 -
Rwork0.282 1833 -
all-1930 -
obs--98.22 %
Refinement TLS params.Method: refined / Origin x: 19.5085 Å / Origin y: 47.4294 Å / Origin z: 22.1964 Å
111213212223313233
T0.0065 Å20.0005 Å20.0069 Å2-0.0108 Å20.0054 Å2--0.0178 Å2
L0.4776 °20.135 °20.2214 °2-0.1956 °20.0577 °2--0.446 °2
S0.0123 Å °-0.0066 Å °0.045 Å °0.0227 Å °-0.0115 Å °0.0073 Å °-0.0201 Å °0.0031 Å °-0.0008 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