[English] 日本語
Yorodumi
- PDB-3tkk: Crystal Structure Analysis of a recombinant predicted acetamidase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tkk
TitleCrystal Structure Analysis of a recombinant predicted acetamidase/ formamidase from the thermophile thermoanaerobacter tengcongensis
ComponentsPredicted acetamidase/formamidase
KeywordsHYDROLASE / Beta/Alpha structure
Function / homologyAcetamidase/Formamidase / Acetamidase/Formamidase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding / Predicted acetamidase/formamidase
Function and homology information
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsQian, M. / Huang, Q. / Wu, G. / Lai, L. / Tang, Y. / Pei, J. / Kusunoki, M.
CitationJournal: PROTEIN J. / Year: 2012
Title: Crystal Structure Analysis of a Recombinant Predicted Acetamidase/Formamidase from the Thermophile Thermoanaerobacter tengcongensis.
Authors: Qian, M. / Huang, Q. / Wu, G. / Lai, L. / Tang, Y. / Pei, J. / Kusunoki, M.
History
DepositionAug 26, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionNov 16, 2011ID: 3MJJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.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_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 / _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: Predicted acetamidase/formamidase
B: Predicted acetamidase/formamidase
C: Predicted acetamidase/formamidase
D: Predicted acetamidase/formamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,15013
Polymers128,6884
Non-polymers4629
Water15,043835
1
A: Predicted acetamidase/formamidase
C: Predicted acetamidase/formamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5957
Polymers64,3442
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-86 kcal/mol
Surface area22400 Å2
MethodPISA
2
B: Predicted acetamidase/formamidase
D: Predicted acetamidase/formamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5556
Polymers64,3442
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-107 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.230, 152.882, 100.255
Angle α, β, γ (deg.)90.00, 99.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: -2 - 299 / Label seq-ID: 1 - 301

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
Predicted acetamidase/formamidase


Mass: 32171.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4T / Gene: TTE1919 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA DE3 / References: UniProt: Q8R8S5
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M calcium acetate, 0.1M sodium cacodylate, 18%(W/V) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 4, 2004 / Details: mirrors
RadiationMonochromator: DOUBLE MIRROR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→99.01 Å / Num. all: 81396 / Num. obs: 75255 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3778 / % possible all: 64.62

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.99→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.291 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23682 3985 5 %RANDOM
Rwork0.17397 ---
all0.178 81396 --
obs0.17716 75255 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.712 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å22.57 Å2
2---2.15 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.99→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9028 0 9 835 9872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0229209
X-RAY DIFFRACTIONr_angle_refined_deg2.2371.97912392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86151196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34126.512344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.637151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2871512
X-RAY DIFFRACTIONr_chiral_restr0.1760.21464
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216664
X-RAY DIFFRACTIONr_mcbond_it1.60225958
X-RAY DIFFRACTIONr_mcangle_it2.46739552
X-RAY DIFFRACTIONr_scbond_it2.32923251
X-RAY DIFFRACTIONr_scangle_it3.38332840
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2257 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.550.5
Bmedium positional0.610.5
Cmedium positional0.50.5
Dmedium positional0.570.5
Amedium thermal1.852
Bmedium thermal1.22
Cmedium thermal1.52
Dmedium thermal1.282
LS refinement shellResolution: 1.99→2.041 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 219 -
Rwork0.242 3778 -
obs-3778 64.62 %
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)
10.7855-0.2056-0.46682.75030.57651.0236-0.01490.0421-0.1547-0.1758-0.0151-0.0372-0.0063-0.04960.030.07450.0073-0.07640.1824-0.01160.27394.62119.5090.785
20.82190.2141-0.22421.9124-0.80941.4945-0.081-0.0946-0.19070.12310.13270.04790.199-0.0997-0.05170.48770.02780.1320.23020.02640.3781-23.41612.57549.438
30.5361-0.6241-0.15713.10680.25990.13460.14140.04260.1682-0.3956-0.037-0.1862-0.2038-0.025-0.10430.28740.0063-0.00070.18050.01030.28282.08451.9564.062
40.8766-0.3368-0.05252.30710.3530.984-0.0844-0.12290.2120.17110.1104-0.013-0.3062-0.0003-0.0260.59290.05440.11480.2393-0.04390.3872-24.17244.64951.888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 299
2X-RAY DIFFRACTION2B1 - 299
3X-RAY DIFFRACTION3C1 - 299
4X-RAY DIFFRACTION4D1 - 299

+
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