[English] 日本語
Yorodumi
- PDB-6c3a: O2-, PLP-dependent L-arginine hydroxylase RohP 4-hydroxy-2-ketoar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c3a
TitleO2-, PLP-dependent L-arginine hydroxylase RohP 4-hydroxy-2-ketoarginine complex
ComponentsUncharacterized protein
KeywordsBIOSYNTHETIC PROTEIN / O2- / PLP-dependent hydroxylase
Function / homology
Function and homology information


biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-EGV / DI(HYDROXYETHYL)ETHER / Aminotransferase class I/classII large domain-containing protein
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsHedges, J.B. / Ryan, K.S.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-03778 Canada
Alfred P. Sloan FoundationFG-20166503 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Snapshots of the Catalytic Cycle of an O2, Pyridoxal Phosphate-Dependent Hydroxylase.
Authors: Hedges, J.B. / Kuatsjah, E. / Du, Y.L. / Eltis, L.D. / Ryan, K.S.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,19116
Polymers95,0242
Non-polymers1,16714
Water16,286904
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint1 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.800, 112.550, 101.970
Angle α, β, γ (deg.)90.000, 96.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-700-

HOH

21B-853-

HOH

31B-952-

HOH

-
Components

#1: Protein Uncharacterized protein


Mass: 47511.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria)
Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057
Gene: SCATT_03970 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8WNK6*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EGV / (4S)-5-carbamimidamido-4-hydroxy-2-oxopentanoic acid


Mass: 189.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11N3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate pH 7, 16-20 % (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.53→52.17 Å / Num. obs: 132732 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 15.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.042 / Rrim(I) all: 0.087 / Net I/σ(I): 9.6 / Num. measured all: 560442 / Scaling rejects: 118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.53-1.564.10.6522695565030.70.3620.7472.1100
8.38-52.1740.04533738360.9950.0270.05321.898.8

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.23data scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJ1

5dj1


Resolution: 1.53→41.687 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1728 6722 5.06 %
Rwork0.1528 125995 -
obs0.1538 132717 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.36 Å2 / Biso mean: 23.486 Å2 / Biso min: 8.94 Å2
Refinement stepCycle: final / Resolution: 1.53→41.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6081 0 77 904 7062
Biso mean--35.48 35.48 -
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066358
X-RAY DIFFRACTIONf_angle_d0.9218639
X-RAY DIFFRACTIONf_chiral_restr0.051966
X-RAY DIFFRACTIONf_plane_restr0.0061107
X-RAY DIFFRACTIONf_dihedral_angle_d6.4625187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.53-1.54740.24572200.240141764396
1.5474-1.56560.23952230.223342094432
1.5656-1.58470.26582150.213141534368
1.5847-1.60480.24292190.205842244443
1.6048-1.62590.21052130.194841854398
1.6259-1.64810.21372220.19541764398
1.6481-1.67170.20252350.185142274462
1.6717-1.69660.18982280.180641234351
1.6966-1.72320.20672320.185142214453
1.7232-1.75140.21152260.183241944420
1.7514-1.78160.20911950.174141914386
1.7816-1.8140.20722170.164242044421
1.814-1.84890.1712430.160541664409
1.8489-1.88660.17951920.154942114403
1.8866-1.92770.17092500.156641824432
1.9277-1.97250.18882100.156242454455
1.9725-2.02180.18072100.156242184428
2.0218-2.07650.16972210.147241884409
2.0765-2.13760.16572400.139741484388
2.1376-2.20660.16392260.138741954421
2.2066-2.28540.14972400.145442124452
2.2854-2.37690.17312060.148742154421
2.3769-2.48510.17452260.148541944420
2.4851-2.61610.16952480.152741664414
2.6161-2.780.16312270.147941854412
2.78-2.99460.17212010.152442544455
2.9946-3.29580.16942590.143142054464
3.2958-3.77250.14132160.138942234439
3.7725-4.75180.1392240.12142234447
4.7518-41.70290.18242380.156742824520
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)
12.72561.3042-0.73511.4098-1.78022.95630.21130.0263-0.6178-0.2496-0.23090.04420.52150.12840.04910.34650.1366-0.07780.3894-0.12260.3438-16.302137.437512.4401
21.0092-0.2162-0.52510.57250.11041.50150.11460.16340.1435-0.1143-0.1295-0.0908-0.13410.07870.0170.15080.04350.02710.12630.03850.1322-2.575358.736218.7786
33.445-0.104-0.46690.6112-0.77541.64920.07760.0423-0.1803-0.0203-0.02590.0081-0.0252-0.0007-0.04560.10690.0347-0.00520.0398-0.02050.1262-16.987145.843336.5693
42.8462-1.48250.82252.8106-1.13631.86630.05520.0179-0.1786-0.0730.04720.16640.0542-0.1976-0.07690.09570.0098-0.01120.115-0.00440.1245-28.116748.049535.5837
51.2834-0.434-0.141.2807-0.24251.74870.05520.09820.0327-0.0498-0.06580.1212-0.138-0.10680.00640.1330.0591-0.00530.1158-0.00690.1356-25.477458.203927.9135
60.8651-0.2342-0.130.6499-0.0950.82210.09060.15810.0836-0.0942-0.0885-0.0049-0.10670.00330.00910.13560.04150.00820.10020.00560.1179-9.272655.783225.539
71.60490.20720.65260.78590.42961.93140.22570.5525-0.1719-0.245-0.16310.2609-0.0466-0.2817-0.01260.24690.1372-0.09590.3577-0.07610.2364-29.463148.08768.6979
80.3867-0.1510.54240.89330.63431.94550.22260.341-0.4566-0.2181-0.1310.37160.5039-0.17670.01040.30970.0599-0.14220.3165-0.16020.4086-29.657535.272713.6145
92.69190.35952.58120.67840.82074.17780.07070.24430.0486-0.1496-0.1502-0.1263-0.06770.16130.10070.19460.08420.03090.19590.0710.13999.144247.0113.9086
100.8457-0.1145-0.0570.7075-0.3391.20050.05690.176-0.1058-0.1537-0.07680.0530.0704-0.02330.02260.13260.0523-0.02120.1122-0.03380.1279-0.708730.503323.4193
114.30890.8147-0.00891.4114-0.27641.10020.02550.14490.2707-0.01530.01320.0912-0.2077-0.1076-0.04060.12050.03860.01340.10210.0050.12871.114238.074442.9495
121.3954-0.2173-0.62361.05910.26941.1897-0.0083-0.0961-0.12590.0163-0.0208-0.04430.14920.17410.02610.10780.0399-0.00850.10430.01670.127112.248825.639543.0737
131.32330.1801-0.33412.5653-0.81591.52430.07440.1437-0.0284-0.072-0.0608-0.1429-0.02210.1876-0.00340.10960.0454-0.00280.1287-0.00540.127312.193827.93530.8411
140.5858-0.27530.03530.5043-0.08370.39620.0490.1653-0.0785-0.0897-0.06820.01220.06080.02140.02170.15180.0492-0.00440.1298-0.02080.12152.162832.212823.8584
151.96791.50951.78992.01611.47783.6439-0.00270.10990.0424-0.1473-0.0262-0.2422-0.16830.4468-0.01130.11150.03840.03880.22090.03220.197526.679342.769330.6951
163.4340.13070.90612.89140.27263.60390.0796-0.34580.42290.2428-0.0385-0.1726-0.44720.2214-0.00480.1439-0.06220.03340.1908-0.0090.171322.63652.920144.0463
171.54350.3028-0.7861.7467-0.90792.42990.14590.0590.2873-0.0113-0.0259-0.0764-0.17430.1838-0.10960.1189-0.01690.0110.12710.01550.177619.617950.688738.0201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 40 )A15 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 93 )A41 - 93
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 119 )A94 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 163 )A120 - 163
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 215 )A164 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 288 )A216 - 288
7X-RAY DIFFRACTION7chain 'A' and (resid 289 through 321 )A289 - 321
8X-RAY DIFFRACTION8chain 'A' and (resid 322 through 390 )A322 - 390
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 59 )B27 - 59
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 108 )B60 - 108
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 132 )B109 - 132
12X-RAY DIFFRACTION12chain 'B' and (resid 133 through 190 )B133 - 190
13X-RAY DIFFRACTION13chain 'B' and (resid 191 through 215 )B191 - 215
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 288 )B216 - 288
15X-RAY DIFFRACTION15chain 'B' and (resid 289 through 321 )B289 - 321
16X-RAY DIFFRACTION16chain 'B' and (resid 322 through 344 )B322 - 344
17X-RAY DIFFRACTION17chain 'B' and (resid 345 through 390 )B345 - 390

+
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