[English] 日本語
Yorodumi
- PDB-4ywr: Structure of a putative phosphomethylpyrimidine kinase from Acine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ywr
TitleStructure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii in non-covalent complex with pyridoxal phosphate
ComponentsPutative hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase
KeywordsTRANSFERASE / putative phosphomethylpyrimidine kinase / pyridoxal phoshpate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / thiamine biosynthetic process
Similarity search - Function
Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / : / Putative hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Biochemistry / Year: 2024
Title: Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate.
Authors: De Vitto, H. / Belfon, K.K.J. / Sharma, N. / Toay, S. / Abendroth, J. / Dranow, D.M. / Lukacs, C.M. / Choi, R. / Udell, H.S. / Willis, S. / Barrera, G. / Beyer, O. / Li, T.D. / Hicks, K.A. / ...Authors: De Vitto, H. / Belfon, K.K.J. / Sharma, N. / Toay, S. / Abendroth, J. / Dranow, D.M. / Lukacs, C.M. / Choi, R. / Udell, H.S. / Willis, S. / Barrera, G. / Beyer, O. / Li, T.D. / Hicks, K.A. / Torelli, A.T. / French, J.B.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9782
Polymers27,7311
Non-polymers2471
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.820, 108.100, 88.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-496-

HOH

21A-624-

HOH

-
Components

#1: Protein Putative hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase


Mass: 27730.598 Da / Num. of mol.: 1 / Fragment: UNP residues 2-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB5075 / Gene: A591_A3049 / Plasmid: AcbaC.00867.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A2TKW6, UniProt: A0A140UHE5*PLUS
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.55 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Microlytics MGSC1 screen, c8: 25% PEG 4000, 200mM ammonium citrate, 100mM Na citrate/HCl, pH 5.6; AcbaC.00867.a.B1.PW37632 at 22 mg/ml; crystal soaked for 2h in reservoir solution with 5mM ...Details: Microlytics MGSC1 screen, c8: 25% PEG 4000, 200mM ammonium citrate, 100mM Na citrate/HCl, pH 5.6; AcbaC.00867.a.B1.PW37632 at 22 mg/ml; crystal soaked for 2h in reservoir solution with 5mM Pyridoxal phosphate, tray 261062, puck hml12-2; cryo: 20% EG

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 12, 2015
RadiationMonochromator: Rigaku Varimaz / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 37353 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.046 / Χ2: 1.009 / Net I/σ(I): 45 / Num. measured all: 595561
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.640.4872.235260278521940.7360.60278.8
1.64-1.690.4443.5411306271626600.8690.50597.9
1.69-1.740.3975.2118066263126290.9330.42999.9
1.74-1.790.3537.6227606254925480.970.371100
1.79-1.850.2879.4528802250325010.9840.30199.9
1.85-1.910.21712.8428905241223900.9910.22799.1
1.91-1.980.15617.7129675233123290.9950.16399.9
1.98-2.070.12422.6529764223122310.9970.129100
2.07-2.160.09133.1232675215021500.9990.094100
2.16-2.260.07946.437359208720580.9990.08198.6
2.26-2.390.06553.1537849195319300.9990.06798.8
2.39-2.530.05562.07389621855185510.056100
2.53-2.70.05170.44407521766176510.05299.9
2.7-2.920.04586.05457101644164410.045100
2.92-3.20.037102.61436311508150810.037100
3.2-3.580.03120.13396171373137310.03100
3.58-4.130.027140.48349571234123210.02799.8
4.13-5.060.023153.01293821042104010.02399.8
5.06-7.160.026133.952310782782710.027100
7.160.02152.371217649148910.0299.6

-
Processing

Software
NameVersionClassification
PHENIXdev_1980refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4yl5

4yl5


Resolution: 1.65→46.181 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1761 1802 5.25 %Random selection
Rwork0.1569 32552 --
obs0.1579 34354 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.35 Å2 / Biso mean: 21.1937 Å2 / Biso min: 6.72 Å2
Refinement stepCycle: final / Resolution: 1.65→46.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 32 240 1903
Biso mean--17.6 32.4 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061757
X-RAY DIFFRACTIONf_angle_d0.8382414
X-RAY DIFFRACTIONf_chiral_restr0.056293
X-RAY DIFFRACTIONf_plane_restr0.005311
X-RAY DIFFRACTIONf_dihedral_angle_d15.621061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69460.22611360.1952445258199
1.6946-1.74450.20851420.178225062648100
1.7445-1.80080.21771510.172924492600100
1.8008-1.86520.22051290.185225052634100
1.8652-1.93990.20841540.19212433258799
1.9399-2.02810.21981490.163424772626100
2.0281-2.13510.17431530.153924762629100
2.1351-2.26880.18811330.16222475260899
2.2688-2.4440.15671280.1492494262299
2.444-2.68990.16291290.152725312660100
2.6899-3.07910.19591280.162925432671100
3.0791-3.8790.15111330.141825572690100
3.879-46.19920.14091370.14126612798100
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)
16.71010.81472.70111.46261.20442.98460.00980.13570.1484-0.10390.0907-0.0193-0.17390.0588-0.13010.1130.00490.01960.06570.00440.0692.081835.317327.6579
25.20316.60883.38128.45993.97683.894-0.15790.0160.3183-0.32680.01990.1233-0.3894-0.03260.11730.14890.00030.01560.08290.00030.09591.119441.514627.3794
34.7431.509-0.03382.2750.18842.16340.01140.0148-0.0156-0.02820.02560.0336-0.0354-0.0861-0.04180.0764-0.0023-0.00320.0654-0.00160.0372-2.035829.647625.955
46.15890.6195-0.48551.77150.0272.49540.1-0.1152-0.32010.0274-0.0590.04830.1824-0.0798-0.01420.1192-0.0032-0.02290.0612-0.00190.0601-0.317323.801327.6478
53.43141.04670.22571.59470.49682.03480.0399-0.08870.00740.05880.01780.00380.11560.04-0.04560.08920.0015-0.0110.07820.0090.06625.237929.45536.4014
63.0040.5413-1.26172.1002-0.26222.41690.0199-0.0642-0.0130.03720.01360.07740.1196-0.0435-0.03050.0948-0.0251-0.01150.08470.00410.0542-2.614530.292346.8402
74.2825-1.75352.07466.4869-2.90126.880.03-0.3140.37750.31560.1120.4234-0.3892-0.3327-0.0970.1508-0.0420.03240.1215-0.03570.1751-4.501439.449251.0071
83.1282-1.0660.94176.51630.91654.66960.0586-0.53350.74570.1991-0.12560.4475-0.3105-0.47590.20510.1904-0.02420.04380.1499-0.03460.2778-2.403246.987348.7549
92.4123-0.8638-0.62515.44731.10154.85830.0053-0.03910.2979-0.065-0.03820.3167-0.2307-0.23550.01420.1633-0.02650.02310.0815-0.04190.15062.301348.370437.5421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 25 )A10 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 39 )A26 - 39
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 52 )A40 - 52
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 74 )A53 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 125 )A75 - 125
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 158 )A126 - 158
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 185 )A159 - 185
8X-RAY DIFFRACTION8chain 'A' and (resid 186 through 204 )A186 - 204
9X-RAY DIFFRACTION9chain 'A' and (resid 205 through 246 )A205 - 246

+
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