[English] 日本語
Yorodumi
- PDB-3qyg: Crystal Structure of Co-type Nitrile Hydratase beta-E56Q from Pse... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qyg
TitleCrystal Structure of Co-type Nitrile Hydratase beta-E56Q from Pseudomonas putida.
Components
  • Co-type Nitrile Hydratase alpha subunit
  • Co-type Nitrile Hydratase beta subunit
KeywordsLYASE / nitrile hydratase / CO / Cobalt / Cysteine Sulfinic Acid
Function / homology
Function and homology information


Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / SH3 type barrels. - #50 / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta ...Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / SH3 type barrels. - #50 / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBrodkin, H.R. / Novak, W.R.P. / Ringe, D. / Petsko, G.A.
CitationJournal: Biochemistry / Year: 2011
Title: Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida.
Authors: Brodkin, H.R. / Novak, W.R. / Milne, A.C. / D'Aquino, J.A. / Karabacak, N.M. / Goldberg, I.G. / Agar, J.N. / Payne, M.S. / Petsko, G.A. / Ondrechen, M.J. / Ringe, D.
History
DepositionMar 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / 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_label_asym_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_label_asym_id / _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: Co-type Nitrile Hydratase alpha subunit
B: Co-type Nitrile Hydratase beta subunit
C: Co-type Nitrile Hydratase alpha subunit
D: Co-type Nitrile Hydratase beta subunit
E: Co-type Nitrile Hydratase alpha subunit
F: Co-type Nitrile Hydratase beta subunit
G: Co-type Nitrile Hydratase alpha subunit
H: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,49216
Polymers194,8888
Non-polymers6048
Water18,9521052
1
A: Co-type Nitrile Hydratase alpha subunit
B: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8734
Polymers48,7222
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-41 kcal/mol
Surface area17200 Å2
MethodPISA
2
C: Co-type Nitrile Hydratase alpha subunit
D: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8734
Polymers48,7222
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-42 kcal/mol
Surface area17250 Å2
MethodPISA
3
E: Co-type Nitrile Hydratase alpha subunit
F: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8734
Polymers48,7222
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-43 kcal/mol
Surface area17070 Å2
MethodPISA
4
G: Co-type Nitrile Hydratase alpha subunit
H: Co-type Nitrile Hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8734
Polymers48,7222
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-43 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.962, 137.549, 85.416
Angle α, β, γ (deg.)90.00, 92.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B and (resseq 1:17 or resseq 22:85 or resseq 103:141 or resseq 143:219 )
211chain D and (resseq 1:17 or resseq 22:85 or resseq 103:141 or resseq 143:219 )
311chain F and (resseq 1:17 or resseq 22:85 or resseq 103:141 or resseq 143:219 )
411chain H and (resseq 1:17 or resseq 22:85 or resseq 103:141 or resseq 143:219 )
112chain A and (resseq 4:43 or resseq 45:52 or resseq...
212chain C and (resseq 4:43 or resseq 45:52 or resseq...
312chain E and (resseq 4:43 or resseq 45:52 or resseq...
412chain G and (resseq 4:43 or resseq 45:52 or resseq...

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Co-type Nitrile Hydratase alpha subunit


Mass: 24667.967 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein
Co-type Nitrile Hydratase beta subunit


Mass: 24053.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1052 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM HEPES pH 7.5 22% Polyacrylic acid 20 mM MgCl2 4% Acetone , VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2007
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.3→45.4 Å / Num. obs: 80874 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 1.8 / Num. unique all: 7283

-
Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IRE

1ire


Resolution: 2.3→45.37 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 4042 5 %
Rwork0.1961 --
obs0.1975 80843 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.476 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.1796 Å2-0 Å23.3423 Å2
2---6.7124 Å2-0 Å2
3---9.3499 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12931 0 28 1052 14011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613474
X-RAY DIFFRACTIONf_angle_d0.9418414
X-RAY DIFFRACTIONf_dihedral_angle_d14.6314801
X-RAY DIFFRACTIONf_chiral_restr0.0742030
X-RAY DIFFRACTIONf_plane_restr0.0042408
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1549X-RAY DIFFRACTIONPOSITIONAL
12D1549X-RAY DIFFRACTIONPOSITIONAL0.055
13F1545X-RAY DIFFRACTIONPOSITIONAL0.046
14H1540X-RAY DIFFRACTIONPOSITIONAL0.046
21A1401X-RAY DIFFRACTIONPOSITIONAL
22C1401X-RAY DIFFRACTIONPOSITIONAL0.046
23E1382X-RAY DIFFRACTIONPOSITIONAL0.035
24G1382X-RAY DIFFRACTIONPOSITIONAL0.036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2974-2.32450.28271170.25342175X-RAY DIFFRACTION78
2.3245-2.35280.31711380.26082341X-RAY DIFFRACTION87
2.3528-2.38260.28961280.26492436X-RAY DIFFRACTION88
2.3826-2.41390.3351420.25382437X-RAY DIFFRACTION90
2.4139-2.4470.28311040.25062492X-RAY DIFFRACTION91
2.447-2.4820.28491150.25212571X-RAY DIFFRACTION92
2.482-2.5190.30111460.2512574X-RAY DIFFRACTION93
2.519-2.55840.28011410.23762539X-RAY DIFFRACTION94
2.5584-2.60030.2631400.24012598X-RAY DIFFRACTION95
2.6003-2.64510.28731710.23792633X-RAY DIFFRACTION96
2.6451-2.69320.24391170.23942673X-RAY DIFFRACTION97
2.6932-2.7450.25041290.22182696X-RAY DIFFRACTION97
2.745-2.8010.29171440.2272656X-RAY DIFFRACTION98
2.801-2.86190.24331480.21982701X-RAY DIFFRACTION98
2.8619-2.92850.28741090.22532759X-RAY DIFFRACTION98
2.9285-3.00170.25051350.21622725X-RAY DIFFRACTION99
3.0017-3.08290.24621410.21352701X-RAY DIFFRACTION99
3.0829-3.17360.24521510.19712750X-RAY DIFFRACTION99
3.1736-3.2760.20541450.19352741X-RAY DIFFRACTION99
3.276-3.3930.18951420.18052727X-RAY DIFFRACTION99
3.393-3.52880.18111330.17172744X-RAY DIFFRACTION100
3.5288-3.68930.1791410.16292766X-RAY DIFFRACTION100
3.6893-3.88380.18571600.16272742X-RAY DIFFRACTION100
3.8838-4.12690.17191680.15542728X-RAY DIFFRACTION100
4.1269-4.44530.17251520.14572747X-RAY DIFFRACTION100
4.4453-4.89220.19411500.13952759X-RAY DIFFRACTION100
4.8922-5.5990.19351310.16022774X-RAY DIFFRACTION100
5.599-7.04990.18211290.16852819X-RAY DIFFRACTION100
7.0499-45.37930.14481750.14942797X-RAY DIFFRACTION100

+
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://pdbjlvh1.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