[English] 日本語
Yorodumi
- PDB-4zgd: Mutant R157A of Fe-Type Nitrile Hydratase from Comamonas testoste... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zgd
TitleMutant R157A of Fe-Type Nitrile Hydratase from Comamonas testosteroni Ni1
Components
  • Nitrile hydratase alpha subunit
  • Nitrile hydratase beta subunit
KeywordsLYASE / Nitrile Hydratase / Iron / Hydrolysis
Function / homology
Function and homology information


nitrile hydratase / nitrile hydratase activity / transition metal ion binding
Similarity search - Function
Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / Nitrile hydratase, beta subunit / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit ...Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / Nitrile hydratase, beta subunit / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, alpha chain / Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily / SH3 type barrels. - #50 / Electron transport accessory-like domain superfamily / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Nitrile hydratase alpha subunit / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsWu, R. / Martinez, S. / Holz, R. / Liu, D.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2015
Title: Analyzing the catalytic role of active site residues in the Fe-type nitrile hydratase from Comamonas testosteroni Ni1.
Authors: Martinez, S. / Wu, R. / Krzywda, K. / Opalka, V. / Chan, H. / Liu, D. / Holz, R.C.
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Data collection / Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrile hydratase alpha subunit
B: Nitrile hydratase beta subunit
C: Nitrile hydratase alpha subunit
D: Nitrile hydratase beta subunit
E: Nitrile hydratase alpha subunit
F: Nitrile hydratase beta subunit
G: Nitrile hydratase alpha subunit
H: Nitrile hydratase beta subunit
I: Nitrile hydratase alpha subunit
J: Nitrile hydratase beta subunit
K: Nitrile hydratase alpha subunit
L: Nitrile hydratase beta subunit
M: Nitrile hydratase alpha subunit
N: Nitrile hydratase beta subunit
O: Nitrile hydratase alpha subunit
P: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,78024
Polymers363,33316
Non-polymers4478
Water53,9552995
1
A: Nitrile hydratase alpha subunit
B: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-51 kcal/mol
Surface area18150 Å2
MethodPISA
2
C: Nitrile hydratase alpha subunit
D: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-46 kcal/mol
Surface area17940 Å2
MethodPISA
3
E: Nitrile hydratase alpha subunit
F: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-49 kcal/mol
Surface area18000 Å2
MethodPISA
4
G: Nitrile hydratase alpha subunit
H: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-49 kcal/mol
Surface area18030 Å2
MethodPISA
5
I: Nitrile hydratase alpha subunit
J: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-52 kcal/mol
Surface area18060 Å2
MethodPISA
6
K: Nitrile hydratase alpha subunit
L: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-49 kcal/mol
Surface area18040 Å2
MethodPISA
7
M: Nitrile hydratase alpha subunit
N: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-51 kcal/mol
Surface area18140 Å2
MethodPISA
8
O: Nitrile hydratase alpha subunit
P: Nitrile hydratase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4723
Polymers45,4172
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-50 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.590, 111.590, 474.604
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein
Nitrile hydratase alpha subunit


Mass: 22836.053 Da / Num. of mol.: 8 / Mutation: R157A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: J9PBS0, nitrile hydratase
#2: Protein
Nitrile hydratase beta subunit


Mass: 22580.586 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: J9PBS1, nitrile hydratase
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2995 / 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: 4.69 Å3/Da / Density % sol: 73.78 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: Hanging Drop with reservoir solution as the following: 1.08 M K2HPO4, 0.49 M NaH2PO4 with 25 or 30% (v/v) glycerol
PH range: 7 / Temp details: Room Temperature

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→50.491 Å / Num. obs: 313740 / % possible obs: 100 % / Redundancy: 3.8 % / Rpim(I) all: 0.093 / Rrim(I) all: 0.182 / Rsym value: 0.156 / Net I/av σ(I): 4.347 / Net I/σ(I): 6.9 / Num. measured all: 1185275
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.25-2.373.70.7241171800458880.4320.7242.1100
2.37-2.523.80.5791.3162598433420.3450.5792.6100
2.52-2.693.80.4321.7153136406720.2570.4323.3100
2.69-2.93.80.2982.5143053379460.1780.2984.4100
2.9-3.183.80.23.6132172349630.1190.26.2100
3.18-3.563.80.1265.4119854315670.0750.1269.4100
3.56-4.113.80.0867.6105713277880.0510.08613100
4.11-5.033.80.079.189586234990.0420.0715.3100
5.03-7.123.80.0649.769330181280.0380.06414.1100
7.12-50.5593.80.052103803399470.0310.05217.299.7

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 2.25→50.491 Å / FOM work R set: 0.8585 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 15125 5.05 %
Rwork0.1725 297626 -
obs0.174 313458 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.98 Å2 / Biso mean: 31.78 Å2 / Biso min: 12.87 Å2
Refinement stepCycle: final / Resolution: 2.25→50.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25536 0 8 2995 28539
Biso mean--32.74 37.7 -
Num. residues----3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726222
X-RAY DIFFRACTIONf_angle_d1.07535686
X-RAY DIFFRACTIONf_chiral_restr0.0433930
X-RAY DIFFRACTIONf_plane_restr0.0054620
X-RAY DIFFRACTIONf_dihedral_angle_d13.0969450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.27560.29815320.27231002710559100
2.2756-2.30240.28485230.2583981710340100
2.3024-2.33040.28375590.2613997010529100
2.3304-2.35990.29565230.2537990210425100
2.3599-2.3910.27685290.2464981910348100
2.391-2.42380.26075110.24081005710568100
2.4238-2.45840.26075560.2353982110377100
2.4584-2.49510.28035200.2339989710417100
2.4951-2.53410.285220.22521004310565100
2.5341-2.57560.2745390.222980210341100
2.5756-2.620.26265220.2182991010432100
2.62-2.66770.2555360.2075994910485100
2.6677-2.7190.24065440.2031996710511100
2.719-2.77450.2345150.1994986810383100
2.7745-2.83480.23855050.1972994810453100
2.8348-2.90070.22764990.1912990110400100
2.9007-2.97320.22695580.1842994910507100
2.9732-3.05360.24765220.191989310415100
3.0536-3.14350.22155130.1803996210475100
3.1435-3.24490.19275310.1676994010471100
3.2449-3.36090.20785300.1642993710467100
3.3609-3.49540.19155480.1615991610464100
3.4954-3.65440.17515060.1471992810434100
3.6544-3.8470.16995040.1418998810492100
3.847-4.0880.15595110.1274989410405100
4.088-4.40340.15145120.1229995210464100
4.4034-4.84630.13335450.117996210507100
4.8463-5.54680.15235600.13986410424100
5.5468-6.98540.16995340.1478992510459100
6.9854-50.50370.15885230.14498181034199

+
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