[English] 日本語
Yorodumi
- PDB-5cm7: Structure of thiamine-monophosphate kinase from Acinetobacter bau... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cm7
TitleStructure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (TPP)
ComponentsThiamine-monophosphate kinase
KeywordsTRANSFERASE / SSGCID / Acinetobacter baumannii / Thiamine-monophosphate kinase / thiamine diphosphate / TPP / adenosine diphosphate / ADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


thiamine-phosphate kinase / thiamine-phosphate kinase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Thiamine-monophosphate kinase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Thiamine-monophosphate kinase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / THIAMINE DIPHOSPHATE / Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2019
Title: Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products.
Authors: Sullivan, A.H. / Dranow, D.M. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E. / Abendroth, J.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiamine-monophosphate kinase
B: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,80918
Polymers68,7202
Non-polymers2,08916
Water13,998777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-216 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.750, 117.120, 55.890
Angle α, β, γ (deg.)90.000, 108.570, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Thiamine-monophosphate kinase / Thiamine-phosphate kinase


Mass: 34359.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: thiL, ABUW_0092 / Plasmid: AcbaC.17905.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D5YC82, thiamine-phosphate kinase

-
Non-polymers , 6 types, 793 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.29 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions Morpheus E5: 30mM each: Diethylene glycol, Triethylene-glycol, Tetraethylene glycol, Pentaethylene glycol; 100mM Imidazole, MES monohydrate (acid); 20% v/v PEG 500 MME; ...Details: Molecular Dimensions Morpheus E5: 30mM each: Diethylene glycol, Triethylene-glycol, Tetraethylene glycol, Pentaethylene glycol; 100mM Imidazole, MES monohydrate (acid); 20% v/v PEG 500 MME; 10% w/v PEG 20000; AnphA.17905.a.B1.PW37686 at 30mg/ml, 5mM each MgCl2, ADO and TPP; cryo: direct; tray 264490e5, puck ute6-11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 22, 2015
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 89068 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 10.94 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.064 / Χ2: 1.015 / Net I/σ(I): 24.47 / Num. measured all: 991836
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.594.20.8820.3763.5526382660962660.42794.8
1.59-1.630.9410.3455.2445655645864420.37299.8
1.63-1.680.9620.3046.1748853623462320.325100
1.68-1.730.9710.2667.2149616607660760.284100
1.73-1.790.9810.2238.750070586658590.23799.9
1.79-1.850.9860.19510.150554570656940.20799.8
1.85-1.920.9930.15112.8451349553855360.159100
1.92-20.9950.12515.7351027529452840.13299.8
2-2.090.9960.10420.1951136508350800.1199.9
2.09-2.190.9970.09223.5250803484448380.09699.9
2.19-2.310.9980.08128.454658466446490.08599.7
2.31-2.450.9980.07433.8357551436243560.07799.9
2.45-2.620.9990.06837.156950410441000.07199.9
2.62-2.830.9990.06242.157356387238640.06499.8
2.83-3.10.9990.05548.9157533353035250.05699.9
3.1-3.470.9990.04961.9861910317831730.0599.8
3.47-410.04472.0858725282728170.04599.6
4-4.910.0475.4349140238623800.04199.7
4.9-6.9310.04272.2940319187518660.04399.5
6.930.9990.03678.8822249104710310.03798.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cc8

5cc8


Resolution: 1.55→44.501 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1674 2021 2.27 %
Rwork0.1419 87009 -
obs0.1425 89030 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.66 Å2 / Biso mean: 17.9481 Å2 / Biso min: 5.71 Å2
Refinement stepCycle: final / Resolution: 1.55→44.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 118 780 5517
Biso mean--11.24 29.25 -
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065040
X-RAY DIFFRACTIONf_angle_d1.0856931
X-RAY DIFFRACTIONf_chiral_restr0.05780
X-RAY DIFFRACTIONf_plane_restr0.005952
X-RAY DIFFRACTIONf_dihedral_angle_d11.293082
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.58880.24031610.19675840600195
1.5888-1.63170.19881510.165162236374100
1.6317-1.67970.1831490.151361906339100
1.6797-1.7340.17911570.148762476404100
1.734-1.79590.17371300.143362336363100
1.7959-1.86780.18311500.146862206370100
1.8678-1.95290.18761370.148162746411100
1.9529-2.05580.18791330.143962056338100
2.0558-2.18460.17111330.140462386371100
2.1846-2.35330.17091200.143362606380100
2.3533-2.59010.17161730.14162216394100
2.5901-2.96480.1551470.145162786425100
2.9648-3.7350.12931260.133862636389100
3.735-44.51920.15441540.127163176471100
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)
11.5203-0.44230.12521.858-0.51260.12220.03930.076-0.0023-0.0827-0.041-0.18590.04550.08760.01320.103-0.00220.00120.1151-0.00510.112655.96016.756861.3425
20.8894-0.00910.24241.1196-0.11620.79820.0036-0.0286-0.0680.10960.0094-0.08240.03320.0209-0.01980.0689-0.004-0.00030.07420.00820.076843.7445-4.405163.3238
32.365-0.59140.78752.7978-0.98833.49420.00790.1151-0.16270.09470.0134-0.2253-0.00520.1998-0.01990.05830.00190.00790.0966-0.01940.141154.2839-7.445760.9505
40.5720.34260.25350.590.22820.28680.00840.0534-0.00840.04530.009-0.03540.01370.015-0.01350.06480.00290.01110.08230.01040.063837.9758-6.829656.8684
50.95640.14970.3431.8430.01290.48660.0250.1276-0.0001-0.0547-0.03780.05130.02080.04120.00480.05050.00010.01820.0876-0.00940.052525.0254-13.139551.1552
60.06330.27750.14361.32120.62640.30630.3236-0.35390.12760.4926-0.24560.08840.3441-0.0983-0.0560.2209-0.08170.06150.2888-0.05120.162320.7937-17.114862.2024
71.5590.3252-1.0540.2836-0.91962.82540.1261-0.15610.14530.21-0.04960.2846-0.1779-0.2599-0.10370.1126-0.00590.02150.1411-0.02320.155129.51589.240464.8604
80.82610.2825-0.07130.96770.03291.14110.0302-0.1460.02110.1127-0.05190.07390.13-0.07470.01380.0896-0.01420.00390.0815-0.00080.066841.981410.328475.1152
91.65120.7835-0.58493.0826-1.55262.24410.0134-0.25120.09410.183-0.04930.29850.0468-0.25410.00610.1108-0.01320.04120.169-0.03650.11831.738512.281179.0933
100.54290.32150.3460.78630.25280.84180.0343-0.080.03620.1357-0.087-0.0316-0.0074-0.01750.03890.09020.0025-0.00320.0760.00220.090547.729217.243976.2251
110.6834-0.09040.16560.9690.37851.7243-0.0068-0.00650.09840.11770.0271-0.1203-0.05730.1650.02290.1078-0.0221-0.0380.10060.00020.133360.350624.715979.1777
120.73131.17550.74851.87151.20650.78440.236-0.0254-0.24780.51730.0967-0.65660.20010.1665-0.22980.2778-0.0126-0.12220.3105-0.00110.333566.235514.958584.8874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 92 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 110 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 189 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 288 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 289 through 305 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 35 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 92 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 110 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 111 through 189 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 190 through 288 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 289 through 305 )B0

+
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