[English] 日本語
Yorodumi
- PDB-4y0a: Shikimate kinase from Acinetobacter baumannii in complex with shi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y0a
TitleShikimate kinase from Acinetobacter baumannii in complex with shikimate
ComponentsShikimate kinase
Keywordstransferase/transferase inhibitor / Shikimate Pathway / Transferase / Nucleoside monophosphate (NMP) kinase family / amino acid biosynthesis / ATP-binding / Kinase / nucleotide binding / transferase-transferase inhibitor complex
Function / homology
Function and homology information


shikimate kinase / shikimate kinase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Shikimate kinase, conserved site / Shikimate kinase signature. / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-SKM / Shikimate kinase / :
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.911 Å
AuthorsSutton, K.A. / Breen, J. / MacDonald, U. / Beanan, J.M. / Olson, R. / Russo, T.A. / Schultz, L.W. / Umland, T.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States) United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of shikimate kinase, an in vivo essential metabolic enzyme in the nosocomial pathogen Acinetobacter baumannii, in complex with shikimate.
Authors: Sutton, K.A. / Breen, J. / MacDonald, U. / Beanan, J.M. / Olson, R. / Russo, T.A. / Schultz, L.W. / Umland, T.C.
History
DepositionFeb 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Data collection
Revision 1.2Apr 10, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8275
Polymers20,3641
Non-polymers4624
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.980, 85.810, 112.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

21A-434-

HOH

31A-451-

HOH

-
Components

#1: Protein Shikimate kinase / / SK


Mass: 20364.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB307-0294 / Gene: aroK, ABBFA_000324 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: B7GVP4, UniProt: A0A0M3KL09*PLUS, shikimate kinase
#2: Chemical ChemComp-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE / Shikimic acid


Mass: 174.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 4.87 Å3/Da / Density % sol: 74.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 1.5M Lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.911→36.02 Å / Num. all: 30525 / Num. obs: 30525 / % possible obs: 98.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 32.28 Å2 / Rpim(I) all: 0.032 / Rrim(I) all: 0.08 / Rsym value: 0.072 / Net I/av σ(I): 5.751 / Net I/σ(I): 12.9 / Num. measured all: 187575
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.91-2.016.10.4361.82664443340.190.4363.396.9
2.01-2.146.20.2523.12565941290.110.2525.697.7
2.14-2.286.20.1634.62460939580.0710.1638.298.1
2.28-2.476.20.11962257436360.0520.11910.898.2
2.47-2.76.20.0986.52098233910.0430.09814.398.6
2.7-3.026.20.0758.51918131070.0330.07517.599
3.02-3.496.10.0659.31678827330.0290.06521.199.1
3.49-4.276.10.05910.41435923550.0270.05923.899.4
4.27-6.0460.05810.31106318470.0260.05824.499.6
6.04-36.025.50.0599.6571610350.0280.05923.496.4

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
SCALA3.3.20data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KAG

1kag


Resolution: 1.911→36.02 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 1507 4.94 %
Rwork0.1915 29017 -
obs0.1936 30524 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.1 Å2 / Biso mean: 46.4057 Å2 / Biso min: 22.5 Å2
Refinement stepCycle: final / Resolution: 1.911→36.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 36 160 1632
Biso mean--41.44 49.63 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021484
X-RAY DIFFRACTIONf_angle_d1.6582008
X-RAY DIFFRACTIONf_chiral_restr0.083229
X-RAY DIFFRACTIONf_plane_restr0.009256
X-RAY DIFFRACTIONf_dihedral_angle_d15.399571
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.911-1.97270.30351170.25322559267696
1.9727-2.04320.24551340.21522606274097
2.0432-2.1250.23881470.18762567271498
2.125-2.22170.20991310.17412613274498
2.2217-2.33880.21711380.17662605274398
2.3388-2.48530.22271410.17792630277198
2.4853-2.67710.2351420.17572607274998
2.6771-2.94640.23451390.1972647278699
2.9464-3.37250.2351420.20252675281799
3.3725-4.24790.23731400.18172709284999
4.2479-36.02680.23781360.19752799293598
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)
12.42440.91771.47992.68580.00131.4329-0.0338-0.16280.1291-0.23420.02650.4326-0.09-0.18780.02050.35640.0077-0.06790.31410.01610.3303-11.342711.74038.9187
27.95352.36096.01754.22391.63185.812-0.1118-0.44140.26140.604-0.23940.2328-0.6281-0.77610.28280.39330.0111-0.02130.2943-0.00220.2621-5.111914.4723.4128
37.86221.56694.32515.9975-1.0648.03670.1225-0.424-0.04140.6222-0.01780.0132-0.31080.0514-0.08620.2942-0.0298-0.00060.26650.05860.24260.77477.304627.0732
47.708-1.8722.13164.5323-2.74452.33990.1276-0.405-0.641-0.24630.15080.53080.3074-0.2822-0.20310.3124-0.0543-0.07060.27570.04670.3107-5.561.818217.0272
54.77233.52770.74386.1893-0.46511.8112-0.41820.37550.0376-1.14960.3146-0.05810.03160.26710.13060.3780.04060.01740.2537-0.00970.2013.41029.12716.8779
60.5377-0.1615-0.1067.5245-1.97128.386-0.0586-0.5418-0.0220.3408-0.0694-0.4103-0.29920.33150.04090.327-0.042-0.03010.46520.07160.461913.524116.624917.6357
73.9682.70072.11778.64151.90855.1250.114-0.0011-0.7645-0.3541-0.1189-0.99970.62230.5363-0.02150.42160.13370.0690.37630.05590.42110.09662.89410.4252
89.04955.1588-0.87914.0446-1.72096.6745-0.3391.3554-0.2063-1.32120.6031-0.6458-0.27670.1443-0.17120.7973-0.03990.03060.4481-0.04630.4055-0.9027.87011.2335
99.24025.07554.51716.02883.79445.206-0.11210.6336-0.4783-0.680.23140.29750.19460.2905-0.13180.51960.0595-0.12750.4119-0.01850.3867-11.56828.6676-1.2347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 44 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 60 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 86 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 110 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 127 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 128 through 141 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 160 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 171 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 172 through 189 )A0

+
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