[English] 日本語
Yorodumi
- PDB-5zss: L-Cysteine-PLP reaction intermediate of NifS from Hydrogenimonas ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zss
TitleL-Cysteine-PLP reaction intermediate of NifS from Hydrogenimonas thermophila
Components(Cysteine desulfurase) x 2
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase
Function / homology
Function and homology information


cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / iron-sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Cysteine desulfurase NifS, proteobacteria / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Cysteine desulfurase NifS, proteobacteria / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C6P / Cysteine desulfurase
Similarity search - Component
Biological speciesHydrogenimonas thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsNakamura, T. / Fujishiro, T. / Takahashi, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K14510 Japan
Japan Society for the Promotion of Science15H04472 Japan
CitationJournal: to be published
Title: X-ray snapshots of two classes of cysteine desulfurase enzymes NifS and SufS
Authors: Nakamura, R. / Fujishiro, T. / Takahashi, Y.
History
DepositionApr 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine desulfurase
B: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7023
Polymers92,3502
Non-polymers3521
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-34 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.200, 138.200, 99.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 203 or resid 205 through 384))
21(chain B and (resid 0 through 203 or resid 205 through 384))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS(chain A and (resid 0 through 203 or resid 205 through 384))AA0 - 2033 - 206
12PHEPHESERSER(chain A and (resid 0 through 203 or resid 205 through 384))AA205 - 384208 - 387
21HISHISHISHIS(chain B and (resid 0 through 203 or resid 205 through 384))BB0 - 2033 - 206
22PHEPHESERSER(chain B and (resid 0 through 203 or resid 205 through 384))BB205 - 384208 - 387

-
Components

#1: Protein Cysteine desulfurase / NifS


Mass: 46060.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This chain A is an reaction intermediate of L-Cysteine-PLP form of NifS.
Source: (gene. exp.) Hydrogenimonas thermophila (bacteria) / Gene: SAMN05216234_11013 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0A1I5NEH3
#2: Protein Cysteine desulfurase / NifS


Mass: 46289.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This chain B is the resting state of NifS molecule.
Source: (gene. exp.) Hydrogenimonas thermophila (bacteria) / Gene: SAMN05216234_11013 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0A1I5NEH3
#3: Chemical ChemComp-C6P / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE / 4-((1-CARBOXY-2-THIOL-ETHYLAMINO)-METHYL)-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM


Mass: 352.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H17N2O7PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium chloride, 0.1M Tris-HCl, 20% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 24, 2017
RadiationMonochromator: Numerical link type double Si(111) crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.17→45.782 Å / Num. obs: 18389 / % possible obs: 100 % / Redundancy: 5.873 % / Biso Wilson estimate: 73.4 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.176 / Rrim(I) all: 0.193 / Χ2: 0.967 / Net I/σ(I): 11.86 / Num. measured all: 210918 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.17-3.275.8740.9772.2131940.8081.07399.8
3.27-3.55.8680.6543.2460530.8760.718100
3.5-45.870.3086.5387790.9670.338100
4-65.8920.12814125960.9930.141100
6-105.8710.05427.1141710.9990.06100
10-45.7825.70.03146.7811220.9990.03499.2

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EG5

1eg5


Resolution: 3.17→45.782 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2379 920 5 %
Rwork0.1878 --
obs0.1904 18385 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.28 Å2 / Biso mean: 71.8332 Å2 / Biso min: 19.41 Å2
Refinement stepCycle: final / Resolution: 3.17→45.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 22 12 6029
Biso mean--88.24 33.18 -
Num. residues----773
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2330X-RAY DIFFRACTION9.051TORSIONAL
12B2330X-RAY DIFFRACTION9.051TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.17-3.33710.35861310.28824782609
3.3371-3.54610.29711310.242225032634
3.5461-3.81980.2651300.213524632593
3.8198-4.20390.23241310.177924812612
4.2039-4.81170.1971310.161724942625
4.8117-6.060.22141310.175825022633
6.06-45.78640.21491350.159625442679
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)
11.7969-1.4797-0.23374.20181.87372.0880.05560.0689-0.0918-0.34160.0214-0.0430.01360.2007-0.10850.4923-0.0760.08090.4640.0570.319815.117561.5942-12.7255
21.91771.04153.89492.9270.70597.44230.25280.40180.107-0.1969-0.0039-0.45550.76410.961-0.25210.49330.12960.13870.46030.00210.574931.970566.6928-1.0669
36.1666-2.58842.43128.85290.06083.6420.0032-0.58350.05390.43980.4096-0.50120.20350.4146-0.44490.4381-0.01750.02830.6309-0.04350.352231.216675.186212.79
42.85-0.76471.37332.40872.23184.2138-0.21680.03750.3414-0.42980.1753-0.7043-0.3180.47880.04540.4481-0.00550.09850.44380.10770.58930.193780.71631.3189
59.9231-1.91694.98353.67851.865.57530.28160.0728-0.29360.04790.09210.00840.04070.6895-0.30150.5290.00610.05460.40730.04640.391524.51668.6499-5.2825
67.30165.55073.14695.96196.00449.1704-0.19790.1234-0.8014-0.62740.8297-1.47610.83190.6404-0.8180.82260.10380.14150.41610.06720.604931.476756.846-4.1287
72.1747-3.5099-2.01044.67742.58874.48540.38330.34890.2236-0.7615-0.2417-0.137-0.8592-0.2317-0.26070.5054-0.11-0.01070.39240.03520.43610.457279.813-8.8509
89.2481-0.8582-2.85085.1820.5425.11070.12650.17790.7717-0.1738-0.28330.0976-1.0191-0.33370.09050.40570.0645-0.09280.3657-0.00640.43157.503689.07058.2693
97.34073.13155.19785.35525.20253.85970.3538-0.5484-0.42190.3587-0.3701-0.1727-0.1091-0.5039-0.02750.5278-0.00690.08490.47690.08640.39642.873679.640512.6946
105.13471.46831.9284.6655.00835.4967-0.2336-0.440.4328-0.43480.37270.0561-0.50390.3968-0.28550.5954-0.06350.03560.4720.09690.387611.243485.741310.3086
114.77630.0943-3.91165.50730.7336.04130.0753-0.04480.22720.3483-0.25380.7973-0.7275-0.29780.25670.51830.115-0.0080.40910.00820.5458-5.792385.433610.2903
121.8901-1.5127-1.69753.32181.97842.65440.1535-0.021-0.1198-0.0719-0.2523-0.15070.3202-0.21370.11670.5413-0.08550.05430.45350.04490.45899.949452.0235-8.0519
134.1121-2.78420.45093.8111-0.11972.2059-0.3604-0.5553-0.16480.81730.2001-0.18580.63810.35980.16250.80110.0325-0.00040.5730.11290.487526.428647.32678.2281
142.31650.45910.75052.8399-1.24032.82110.0477-0.544-0.44790.88650.0955-0.2221.40720.3868-0.10861.23880.20290.06210.61830.18440.754627.473136.29379.8077
154.3527-0.6684.2670.87940.93464.87420.0294-0.6173-0.20790.37470.31380.03450.4756-0.2779-0.40880.6559-0.03740.14520.48540.09130.452719.526652.80037.0005
161.6854-1.8367-2.73436.53873.33083.2478-0.4052-0.181-1.00560.3402-0.28170.74940.96250.09430.631.00010.03830.09790.52280.13180.744219.366230.9206-9.4473
174.9859-1.65460.884.19682.15933.1121-0.2911-0.0657-0.83810.37340.2345-0.41720.67120.760.11920.73590.11610.14420.52490.13560.651132.058332.2962-14.3202
184.2809-0.8534-2.68964.6062-0.42776.8802-0.16110.854-1.23250.1858-0.75530.32980.3313-0.24720.88110.8115-0.03050.05470.338-0.11680.83626.148428.9395-26.7509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 57 )A-1 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 86 )A58 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 131 )A87 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 201 )A132 - 201
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 221 )A202 - 221
6X-RAY DIFFRACTION6chain 'A' and (resid 222 through 241 )A222 - 241
7X-RAY DIFFRACTION7chain 'A' and (resid 242 through 278 )A242 - 278
8X-RAY DIFFRACTION8chain 'A' and (resid 279 through 305 )A279 - 305
9X-RAY DIFFRACTION9chain 'A' and (resid 306 through 329 )A306 - 329
10X-RAY DIFFRACTION10chain 'A' and (resid 330 through 360 )A330 - 360
11X-RAY DIFFRACTION11chain 'A' and (resid 361 through 386 )A361 - 386
12X-RAY DIFFRACTION12chain 'B' and (resid 0 through 36 )B0 - 36
13X-RAY DIFFRACTION13chain 'B' and (resid 37 through 131 )B37 - 131
14X-RAY DIFFRACTION14chain 'B' and (resid 132 through 201 )B132 - 201
15X-RAY DIFFRACTION15chain 'B' and (resid 202 through 241 )B202 - 241
16X-RAY DIFFRACTION16chain 'B' and (resid 242 through 305 )B242 - 305
17X-RAY DIFFRACTION17chain 'B' and (resid 306 through 360 )B306 - 360
18X-RAY DIFFRACTION18chain 'B' and (resid 361 through 384 )B361 - 384

+
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