[English] 日本語
Yorodumi
- PDB-2a6a: Crystal structure of Glycoprotein endopeptidase (tm0874) from THE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a6a
TitleCrystal structure of Glycoprotein endopeptidase (tm0874) from THERMOTOGA MARITIMA at 2.50 A resolution
Componentshypothetical protein TM0874
KeywordsHYDROLASE / tm0874 / Glycoprotein endopeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine modification / cytosol
Similarity search - Function
Nucleotidyltransferase; domain 5 - #200 / tRNA threonylcarbamoyl adenosine modification protein TsaB / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / : / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 A resolution.
Authors: Xu, Q. / McMullan, D. / Jaroszewski, L. / Krishna, S.S. / Elsliger, M.A. / Yeh, A.P. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chiu, H.J. / Clayton, T. / Duan, L. / ...Authors: Xu, Q. / McMullan, D. / Jaroszewski, L. / Krishna, S.S. / Elsliger, M.A. / Yeh, A.P. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chiu, H.J. / Clayton, T. / Duan, L. / Feuerhelm, J. / Grant, J. / Han, G.W. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Reyes, R. / Rife, C.L. / van den Bedem, H. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJul 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL UNIT IS A TETRAMER WITH 222 POINT SYMMETRY, FORMED BY CRYSTALLOGRAPHIC SYMMETRY, AS ADJUDGED BY EXTENSIVE HYDROPHOBIC CONTACTS BETWEEN THESE UNITS.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein TM0874
B: hypothetical protein TM0874


Theoretical massNumber of molelcules
Total (without water)49,2464
Polymers49,2462
Non-polymers02
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-20 kcal/mol
Surface area16950 Å2
MethodPISA
2
A: hypothetical protein TM0874
B: hypothetical protein TM0874

A: hypothetical protein TM0874
B: hypothetical protein TM0874


Theoretical massNumber of molelcules
Total (without water)98,4938
Polymers98,4934
Non-polymers04
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area8190 Å2
ΔGint-53 kcal/mol
Surface area32040 Å2
MethodPISA
3
A: hypothetical protein TM0874
B: hypothetical protein TM0874

A: hypothetical protein TM0874
B: hypothetical protein TM0874


Theoretical massNumber of molelcules
Total (without water)98,4938
Polymers98,4934
Non-polymers04
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area7530 Å2
ΔGint-48 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.272, 217.112, 51.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 187 / Label seq-ID: 13 - 199

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsTHE BIOLOGICAL UNIT IS A TETRAMER WITH 222 POINT SYMMETRY, FORMED BY CRYSTALLOGRAPHIC SYMMETRY, AS ADJUDGED BY EXTENSIVE HYDROPHOBIC CONTACTS BETWEEN THESE UNITS.

-
Components

#1: Protein hypothetical protein TM0874 / Glycoprotein endopeptidase


Mass: 24623.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0874 / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: GenBank: 15643636, UniProt: Q9WZX7*PLUS
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.25 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 10.0% MPD, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979413, 0.918370
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794131
20.918371
ReflectionResolution: 2.5→29.24 Å / Num. obs: 18685 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.5-2.6499.93.70.4691.627030.469
2.64-2.899.83.70.3292.325330.329
2.8-2.9999.63.70.2053.723730.205
2.99-3.231003.60.126622780.126
3.23-3.541003.60.06810.920480.068
3.54-3.9599.93.60.0421619030.042
3.95-4.561003.50.03715.916700.037
4.56-5.5999.73.50.03118.814430.031
5.59-7.9199.63.40.0232511220.023
7.91-29.249330.01834.46120.018

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 18.431 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.242
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.235 955 5.1 %RANDOM
Rwork0.191 ---
all0.193 ---
obs-17730 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.618 Å2
Baniso -1Baniso -2Baniso -3
1--4.52 Å20 Å20 Å2
2---1.12 Å20 Å2
3---5.65 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 7 22 2889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222909
X-RAY DIFFRACTIONr_bond_other_d0.0010.022806
X-RAY DIFFRACTIONr_angle_refined_deg1.6882.0043955
X-RAY DIFFRACTIONr_angle_other_deg0.85236482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51224.118102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7415497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7751515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02532
X-RAY DIFFRACTIONr_nbd_refined0.2270.2589
X-RAY DIFFRACTIONr_nbd_other0.1820.22741
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21432
X-RAY DIFFRACTIONr_nbtor_other0.0880.21886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4660.24
X-RAY DIFFRACTIONr_mcbond_it2.1731950
X-RAY DIFFRACTIONr_mcbond_other0.493773
X-RAY DIFFRACTIONr_mcangle_it3.35253064
X-RAY DIFFRACTIONr_scbond_it5.66481075
X-RAY DIFFRACTIONr_scangle_it7.84611891
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2742 / Refine-ID: X-RAY DIFFRACTION

RmsTypeWeight
0.52LOOSE POSITIONAL5
2.4LOOSE THERMAL10
LS refinement shellResolution: 2.5→2.588 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.375 84 -
Rwork0.267 1738 -
obs--99.95 %
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)
14.37710.09820.49134.561-1.0341.9567-0.1288-0.34950.45710.34360.0587-0.0228-0.2842-0.1120.0702-0.07260.0733-0.038-0.04260.0488-0.073214.240988.22029.5434
23.1286-0.12050.87472.58670.68272.951-0.117-0.1632-0.15320.11520.0225-0.0057-0.1090.00490.0945-0.06890.0115-0.0208-0.1640.0588-0.315829.885968.866312.5753
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 19313 - 205
22BB0 - 18712 - 199

+
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