[English] 日本語
Yorodumi
- PDB-5j99: Ambient temperature transition state structure of arginine kinase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j99
TitleAmbient temperature transition state structure of arginine kinase - crystal 8/Form I
ComponentsArginine kinase
KeywordsTRANSFERASE / Ambient / Temperature / Arginine / Kinase
Function / homology
Function and homology information


arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain ...Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ARGININE / NITRATE ION / Arginine kinase
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGodsey, M. / Davulcu, O. / Nix, J. / Skalicky, J.J. / Bruschweiler, R. / Chapman, M.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM77643 United States
CitationJournal: Structure / Year: 2016
Title: The Sampling of Conformational Dynamics in Ambient-Temperature Crystal Structures of Arginine Kinase.
Authors: Godsey, M.H. / Davulcu, O. / Nix, J.C. / Skalicky, J.J. / Bruschweiler, R.P. / Chapman, M.S.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9385
Polymers40,2501
Non-polymers6894
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-14 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.871, 66.035, 86.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Arginine kinase / AK


Mass: 40249.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab)
Production host: Escherichia coli (E. coli) / References: UniProt: P51541, arginine kinase

-
Non-polymers , 5 types, 218 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25 mM HEPES, pH 7.5 18% PEG 6000

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→35.908 Å / Num. obs: 36646 / % possible obs: 98 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 29.6
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1 / % possible all: 71

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M15

1m15


Resolution: 1.7→35.908 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.46
RfactorNum. reflection% reflection
Rfree0.1832 1121 3.06 %
Rwork0.1492 --
obs0.1502 36646 89.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→35.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 44 214 3075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123057
X-RAY DIFFRACTIONf_angle_d1.4794132
X-RAY DIFFRACTIONf_dihedral_angle_d15.7341194
X-RAY DIFFRACTIONf_chiral_restr0.068461
X-RAY DIFFRACTIONf_plane_restr0.007526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.77740.35351160.28373481X-RAY DIFFRACTION71
1.7774-1.87110.28481270.24863701X-RAY DIFFRACTION76
1.8711-1.98830.23621380.19864165X-RAY DIFFRACTION84
1.9883-2.14180.20731280.16154579X-RAY DIFFRACTION92
2.1418-2.35730.17161460.14914725X-RAY DIFFRACTION95
2.3573-2.69830.19961450.15374858X-RAY DIFFRACTION98
2.6983-3.39920.18221670.14614961X-RAY DIFFRACTION99
3.3992-35.91580.1461540.12155055X-RAY DIFFRACTION97
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)
11.64030.23790.5531.76010.26232.3169-0.15160.11890.4534-0.3793-0.02880.4217-0.549-0.2976-0.12480.31120.0632-0.09470.2932-0.00450.3468-19.5788.28313.2
21.03080.2854-0.16731.6820.53721.7320.0557-0.2184-0.07850.3298-0.0750.22970.1556-0.194800.1907-0.01550.03640.2476-0.00420.1771-16.274-4.63532.629
30.68550.97710.18221.42980.44381.0089-0.047-0.4686-0.00820.25070.2173-0.6109-0.25230.962-0.08950.29050.0311-0.11690.3735-0.08020.26171.866-4.85632.283
41.6751-0.2479-0.09232.04950.53751.9712-0.01050.1161-0.2458-0.0825-0.01530.05650.2471-0.0727-0.02650.17950.0015-0.03940.1152-0.02720.1726-7.532-16.9515.607
50.6754-1.0039-0.02791.49760.04320.370.08570.42910.485-0.4612-0.0317-0.3462-0.39110.1450.05080.29810.01580.01580.27040.02090.2468-1.232-5.4396.358
65.87196.8625-4.96289.5591-3.26188.3961-0.0981-0.0134-0.0443-0.077-0.1362-0.14390.25590.04460.09430.61230.04720.13850.38010.05760.335-10.1152.89615.803
72.1262.18942.00992.80051.67032.1944-0.5475-0.23850.87951.31160.19810.8131.49490.53270.31450.71290.14410.50170.76860.10031.3181-9.218-3.07918.103
83.71420.91023.08483.71893.02774.6494-0.01-0.05870.13750.15880.2876-0.33640.0947-0.0131-0.05880.18970.0464-0.04610.259-0.01530.1922-0.294-10.42819.224
98.8677-1.00854.35734.7301-4.20945.13340.0204-0.04830.17150.04740.10770.21960.08570.04380.02070.20430.0208-0.04590.2241-0.02470.2784-1.64-6.16921.598
104.39093.43270.17388.9345-4.4473.37640.1184-0.8353-0.3274-0.1917-0.4964-0.05480.07880.07690.40750.13890.01150.0070.2065-0.01730.268-6.149-4.97219.67
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and ( resseq 2:102 or resseq 193:201 or resseq 269:276 )A2 - 102
2X-RAY DIFFRACTION1chain A and ( resseq 2:102 or resseq 193:201 or resseq 269:276 )A193 - 201
3X-RAY DIFFRACTION1chain A and ( resseq 2:102 or resseq 193:201 or resseq 269:276 )A269 - 276
4X-RAY DIFFRACTION2chain A and ( resseq 129:155 or resseq 167:173 or resseq 202:213 or resseq 221:229 or resseq 258:259 )A129 - 155
5X-RAY DIFFRACTION2chain A and ( resseq 129:155 or resseq 167:173 or resseq 202:213 or resseq 221:229 or resseq 258:259 )A167 - 173
6X-RAY DIFFRACTION2chain A and ( resseq 129:155 or resseq 167:173 or resseq 202:213 or resseq 221:229 or resseq 258:259 )A202 - 213
7X-RAY DIFFRACTION2chain A and ( resseq 129:155 or resseq 167:173 or resseq 202:213 or resseq 221:229 or resseq 258:259 )A221 - 229
8X-RAY DIFFRACTION2chain A and ( resseq 129:155 or resseq 167:173 or resseq 202:213 or resseq 221:229 or resseq 258:259 )A258 - 259
9X-RAY DIFFRACTION3chain A and ( resseq 174:187 )A174 - 187
10X-RAY DIFFRACTION4chain A and ( resseq 103:128 or resseq 156:166 or resseq 216:220 or resseq 233:257 or resseq 260:268 or resseq 277:290 or resseq 330:357 )A103 - 128
11X-RAY DIFFRACTION4chain A and ( resseq 103:128 or resseq 156:166 or resseq 216:220 or resseq 233:257 or resseq 260:268 or resseq 277:290 or resseq 330:357 )A156 - 166
12X-RAY DIFFRACTION4chain A and ( resseq 103:128 or resseq 156:166 or resseq 216:220 or resseq 233:257 or resseq 260:268 or resseq 277:290 or resseq 330:357 )A216 - 220
13X-RAY DIFFRACTION4chain A and ( resseq 103:128 or resseq 156:166 or resseq 216:220 or resseq 233:257 or resseq 260:268 or resseq 277:290 or resseq 330:357 )A233 - 257
14X-RAY DIFFRACTION4chain A and ( resseq 103:128 or resseq 156:166 or resseq 216:220 or resseq 233:257 or resseq 260:268 or resseq 277:290 or resseq 330:357 )A260 - 268
15X-RAY DIFFRACTION4chain A and ( resseq 103:128 or resseq 156:166 or resseq 216:220 or resseq 233:257 or resseq 260:268 or resseq 277:290 or resseq 330:357 )A277 - 290
16X-RAY DIFFRACTION4chain A and ( resseq 103:128 or resseq 156:166 or resseq 216:220 or resseq 233:257 or resseq 260:268 or resseq 277:290 or resseq 330:357 )A330 - 357
17X-RAY DIFFRACTION5chain A and ( resseq 293:310 or resseq 321:329 )A293 - 310
18X-RAY DIFFRACTION5chain A and ( resseq 293:310 or resseq 321:329 )A321 - 329
19X-RAY DIFFRACTION6chain A and resseq 402A402
20X-RAY DIFFRACTION7chain A and resseq 403A403
21X-RAY DIFFRACTION8chain A and ( resseq 400 and ( name N1 or name C2 or name N3 or name C4 or name C5 or name C6 or name N6 or name N7 or name C8 or name N9 ) )A400
22X-RAY DIFFRACTION9chain A and ( resseq 400 and ( name C1' or name C2' or name O2' or name C3' or name O3' or name C4' or name O4' or name C5' or name O5' ) )A400
23X-RAY DIFFRACTION10chain A and ( resseq 400 and ( name PA or name O1A or name O2A or name O3A or name PB or name O1B or name O2B or name O3B ) )A400

+
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