[English] 日本語
Yorodumi
- PDB-6pjw: Adenylate kinase from Methanococcus igneus - AMP bound form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pjw
TitleAdenylate kinase from Methanococcus igneus - AMP bound form
ComponentsAdenylate kinase
KeywordsTRANSFERASE / adenylate kinase
Function / homology
Function and homology information


adenylate kinase / adenylate kinase activity / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase AdkA / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesMethanotorris igneus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMoon, S. / Kim, J. / Olmos, J.L. / Bae, E. / Phillips Jr., G.N.
Funding support Korea, Republic Of, United States, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)PJ013181 Korea, Republic Of
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: To Be Published
Title: Adenylate kinase from Methanococcus igneus - AMP bound form
Authors: Bae, E.
History
DepositionJun 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._audit_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
G: Adenylate kinase
H: Adenylate kinase
I: Adenylate kinase
J: Adenylate kinase
K: Adenylate kinase
L: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,63748
Polymers270,01212
Non-polymers8,62536
Water4,035224
1
A: Adenylate kinase
B: Adenylate kinase
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,65912
Polymers67,5033
Non-polymers2,1569
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-73 kcal/mol
Surface area23430 Å2
MethodPISA
2
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,65912
Polymers67,5033
Non-polymers2,1569
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-71 kcal/mol
Surface area23380 Å2
MethodPISA
3
G: Adenylate kinase
H: Adenylate kinase
I: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,65912
Polymers67,5033
Non-polymers2,1569
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-79 kcal/mol
Surface area23920 Å2
MethodPISA
4
J: Adenylate kinase
K: Adenylate kinase
L: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,65912
Polymers67,5033
Non-polymers2,1569
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-75 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.770, 121.390, 121.040
Angle α, β, γ (deg.)90.00, 102.95, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Adenylate kinase / / AK / ATP-AMP transphosphorylase


Mass: 22501.016 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanotorris igneus (archaea) / Gene: adkA, adk / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43408, adenylate kinase
#2: Chemical...
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 4 mM AMP, 8% (w/v) polyethylene glycol 8000, 100 mM magnesium acetate, and 100 mM sodium acetate pH 4.5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 5, 2016 / Details: Rh coated Torroidal Mirror
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.4→48 Å / Num. obs: 92418 / % possible obs: 94.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 56.5 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.85
Reflection shellResolution: 2.4→2.54 Å / Mean I/σ(I) obs: 0.74 / Num. unique obs: 4948 / CC1/2: 0.249 / % possible all: 72

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDS20170923data reduction
XSCALE20170923data scaling
PHENIXphasing
Coot1.15.2_3472model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.328 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.97
RfactorNum. reflection% reflection
Rfree0.2479 2016 2.19 %
Rwork0.2002 --
obs0.2013 92197 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→44.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17844 0 564 224 18632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01618672
X-RAY DIFFRACTIONf_angle_d1.56625284
X-RAY DIFFRACTIONf_dihedral_angle_d12.41311712
X-RAY DIFFRACTIONf_chiral_restr0.0693024
X-RAY DIFFRACTIONf_plane_restr0.013444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45920.35151000.33854404X-RAY DIFFRACTION65
2.4592-2.52570.33541000.32225110X-RAY DIFFRACTION75
2.5257-2.60.3711010.29455831X-RAY DIFFRACTION85
2.6-2.68390.34842020.27736507X-RAY DIFFRACTION96
2.6839-2.77980.30531010.25716832X-RAY DIFFRACTION100
2.7798-2.89110.2962020.24456768X-RAY DIFFRACTION100
2.8911-3.02260.27681010.23536863X-RAY DIFFRACTION100
3.0226-3.18190.28372020.24186791X-RAY DIFFRACTION100
3.1819-3.38120.30871010.23846842X-RAY DIFFRACTION100
3.3812-3.64220.29312020.20936782X-RAY DIFFRACTION100
3.6422-4.00850.27071010.18316900X-RAY DIFFRACTION100
4.0085-4.5880.2032010.16136796X-RAY DIFFRACTION100
4.588-5.77840.19181010.16866939X-RAY DIFFRACTION100
5.7784-330.20112010.16456816X-RAY DIFFRACTION99
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)
13.7245-0.13270.57994.11810.04483.20540.08710.90710.0799-0.69210.06480.5441-0.0816-0.4604-0.07920.44160.0829-0.04760.63570.05770.504817.88981.252332.6457
23.51810.2452-0.05955.0530.88112.87890.0751-0.1087-0.18570.2838-0.0241-0.58890.460.0354-0.01320.31560.0395-0.04080.23860.00650.444835.8374-12.792854.4415
33.9930.516-1.16454.17471.37775.32570.20110.30050.6963-0.41450.1604-0.6588-0.94450.29220.0290.4636-0.020.14330.26140.06460.709338.133318.251649.4866
43.4020.31910.50463.66790.10033.45260.05090.5296-0.1817-0.32930.03340.48080.0425-0.412-0.04420.3620.0788-0.06090.4042-0.08240.38345.3372-3.210692.7523
53.51610.65290.31865.4040.32012.9780.0725-0.156-0.3780.48420.0212-0.66190.51240.4461-0.00270.44920.1202-0.07760.3171-0.00680.448568.1534-12.1314112.5265
63.23410.3001-1.46873.66041.26294.38210.18070.23040.5767-0.31050.0692-0.333-0.71870.086-0.06650.53330.03030.04480.24420.03420.457764.878318.284105.063
73.5449-0.082-0.86633.9637-0.59872.7571-0.05130.47190.78540.24880.53890.7891-0.685-0.875-0.06640.67610.35820.09360.84260.30780.574953.433820.45389.4687
83.44740.4145-0.4094.0142-0.29824.3647-0.135-0.71060.10040.76930.2913-0.5635-0.23340.2062-0.07060.64870.2417-0.08510.6511-0.05310.380176.00489.193128.3942
93.50840.54080.5263.4039-0.71414.30530.0790.2273-0.66650.07350.08420.42650.5607-0.5782-0.12570.50920.05080.05680.69010.02330.488655.2891-10.534415.294
105.0423-0.1102-0.6063.6177-0.014.5932-0.2664-1.20380.01440.80280.1503-0.28690.0926-0.03620.05810.42990.1472-0.08350.7171-0.03580.3122102.08538.049786.7251
113.925-0.59930.323.4337-0.13984.20680.0995-0.2489-0.8322-0.0386-0.21590.75971.3465-1.1225-0.02510.6465-0.28820.04130.7823-0.10720.617381.2242-6.57468.2644
124.5586-0.45340.88873.78590.31164.2057-0.23930.09890.6264-0.16650.02170.2104-0.7065-0.55030.07270.38750.1364-0.06810.5876-0.11490.43285.409424.354465.6498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'
7X-RAY DIFFRACTION7chain 'G'
8X-RAY DIFFRACTION8chain 'H'
9X-RAY DIFFRACTION9chain 'I'
10X-RAY DIFFRACTION10chain 'J'
11X-RAY DIFFRACTION11chain 'K'
12X-RAY DIFFRACTION12chain 'L'

+
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