[English] 日本語
Yorodumi
- PDB-2pfe: Crystal Structure of Thermobifida fusca Protease A (TFPA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pfe
TitleCrystal Structure of Thermobifida fusca Protease A (TFPA)
ComponentsAlkaline serine protease
Keywordshydrolase/hydrolase inhibitor / Beta-barrels / serine protease / thermophile / Kinetic Stability / thermostability / protein folding / alpha-lytic protease / folding transition state structure / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


serine-type endopeptidase activity / extracellular region
Similarity search - Function
Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H ...Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / Alkaline serine protease / Streptogrisin C. Serine peptidase. MEROPS family S01A
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.436 Å
AuthorsKelch, B.A. / Agard, D.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Mesophile versus Thermophile: Insights Into the Structural Mechanisms of Kinetic Stability
Authors: Kelch, B.A. / Agard, D.A.
History
DepositionApr 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jun 6, 2012Group: Non-polymer description
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Apr 3, 2024Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Alkaline serine protease
B: Alkaline serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6588
Polymers37,8762
Non-polymers7836
Water6,395355
1
A: Alkaline serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3294
Polymers18,9381
Non-polymers3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkaline serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3294
Polymers18,9381
Non-polymers3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Alkaline serine protease
hetero molecules

B: Alkaline serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6588
Polymers37,8762
Non-polymers7836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_547-x+1/2,y-1/2,-z+21
Buried area2040 Å2
ΔGint-34 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.959, 68.552, 40.355
Angle α, β, γ (deg.)90.00, 101.98, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit.

-
Components

#1: Protein Alkaline serine protease / Protease A / TFPA


Mass: 18937.787 Da / Num. of mol.: 2 / Fragment: residues 183-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX
Description: Secreted with N-terminal, covalently attached Pro region necessary for folding and secretion
Gene: tfpA / Plasmid: pGL-1 / Production host: Streptomyces lividans (bacteria) / References: UniProt: O86984, UniProt: Q47SP5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF / AEBSF


Mass: 203.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% (v/v) glycerol, 10mM MnCl2, 0.15M AmSO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2004
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.436→50 Å / Num. all: 63419 / Num. obs: 61453 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.52
Reflection shellResolution: 1.436→1.46 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2754 / % possible all: 87.8

-
Processing

Software
NameVersionClassification
REFMAC5.2refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2.1A structure of TFPA

Resolution: 1.436→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.498 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.083 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TLS refinement used
RfactorNum. reflection% reflectionSelection details
Rfree0.22898 6073 10.1 %RANDOM
Rwork0.20205 ---
all0.2048 55164 --
obs0.2048 53796 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.462 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.24 Å2
2---0.21 Å20 Å2
3---0.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.082 Å0.083 Å
Refinement stepCycle: LAST / Resolution: 1.436→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 46 355 3039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212784
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9433789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.13322.24598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.63115375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3891520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022134
X-RAY DIFFRACTIONr_nbd_refined0.1990.21356
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21950
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2301
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.222
X-RAY DIFFRACTIONr_mcbond_it0.6681.51845
X-RAY DIFFRACTIONr_mcangle_it1.0422918
X-RAY DIFFRACTIONr_scbond_it1.77431070
X-RAY DIFFRACTIONr_scangle_it2.5234.5870
LS refinement shellResolution: 1.436→1.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 306 -
Rwork0.284 3155 -
obs--89.64 %
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)
11.29010.2736-0.03391.02130.07081.1271-0.00470.09810.0112-0.05430.0715-0.0811-0.07320.1368-0.0668-0.0532-0.0087-0.0134-0.0199-0.0109-0.0437.23815.05849.388
21.31830.46130.01011.6699-0.0561.1919-0.0880.1636-0.003-0.18190.12070.10190.0926-0.0845-0.0327-0.0372-0.0232-0.037-0.01670.0103-0.047612.61312.43623.525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 2451 - 186
2X-RAY DIFFRACTION2BB15 - 2451 - 186

+
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