[English] 日本語
Yorodumi
- PDB-7t5a: Crystal structure of the molybdate-binding periplasmic protein Mo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t5a
TitleCrystal structure of the molybdate-binding periplasmic protein ModA from the bacteria Pseudomonsa aeruginosa in tungstate-bound form
ComponentsMolybdate-binding periplasmic protein ModA
KeywordsMETAL BINDING PROTEIN / Molybdate-binding periplasmic protein
Function / homologyAMMONIUM ION / TUNGSTATE(VI)ION
Function and homology information
Biological speciesPseudomonas aeruginosa PA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsNgu, D.H.Y. / Luo, Z. / Lim, B.Y.J. / Kobe, B.
Funding support Australia, 7items
OrganizationGrant numberCountry
Australian Research Council (ARC)LE170100200 Australia
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1122582 Australia
National Health and Medical Research Council (NHMRC, Australia)1180826 Australia
Australian Research Council (ARC)DP170102102 Australia
Australian Research Council (ARC)FL180100109 Australia
Australian Research Council (ARC)FT170100006 Australia
CitationJournal: Front Microbiol / Year: 2022
Title: The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis.
Authors: Maunders, E.A. / Ngu, D.H.Y. / Ganio, K. / Hossain, S.I. / Lim, B.Y.J. / Leeming, M.G. / Luo, Z. / Tan, A. / Deplazes, E. / Kobe, B. / McDevitt, C.A.
History
DepositionDec 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Molybdate-binding periplasmic protein ModA
B: Molybdate-binding periplasmic protein ModA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3278
Polymers48,7592
Non-polymers5686
Water2,450136
1
A: Molybdate-binding periplasmic protein ModA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6453
Polymers24,3791
Non-polymers2662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Molybdate-binding periplasmic protein ModA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6815
Polymers24,3791
Non-polymers3024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.115, 40.977, 111.038
Angle α, β, γ (deg.)90.000, 92.530, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 23 through 251 or resid 321 through 322))
d_2ens_1(chain "B" and (resid 23 through 251 or resid 321 through 322))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALALEUA2 - 230
d_12ens_1WO4WO4B
d_21ens_1ALALEUD1 - 229
d_22ens_1WO4WO4E

NCS oper: (Code: givenMatrix: (0.999910500362, -0.00276081946134, 0.0130908037458), (-0.00293314045042, -0.999909066676, 0.0131626390484), (0.0130532736854, -0.013199858163, -0.999827673047)Vector: ...NCS oper: (Code: given
Matrix: (0.999910500362, -0.00276081946134, 0.0130908037458), (-0.00293314045042, -0.999909066676, 0.0131626390484), (0.0130532736854, -0.013199858163, -0.999827673047)
Vector: 21.2881962933, 4.23541433907, -55.5188940358)

-
Components

#1: Protein Molybdate-binding periplasmic protein ModA


Mass: 24379.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The ligand-free ModA protein was chemically modified via reductive alkylation of surface lysine residues prior to co-crystallisation with tungstate.
Source: (gene. exp.) Pseudomonas aeruginosa PA1 (bacteria) / Strain: Laboratory strain PAO1 / Gene: modA / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 2.2 M ammonium sulfate, 25% v/v glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.16→46.07 Å / Num. obs: 22601 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 24.01 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.07 / Rrim(I) all: 0.193 / Χ2: 1 / Net I/σ(I): 9.5
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1945 / CC1/2: 0.715 / CC star: 0.909 / Rpim(I) all: 0.359 / Rrim(I) all: 0.94 / Χ2: 1.01 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATG

1atg


Resolution: 2.16→43.23 Å / SU ML: 0.283 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2141
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2637 1197 5.3 %
Rwork0.2296 21367 -
obs0.2314 22564 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.72 Å2
Refinement stepCycle: LAST / Resolution: 2.16→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 14 136 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01893502
X-RAY DIFFRACTIONf_angle_d1.30534757
X-RAY DIFFRACTIONf_chiral_restr0.1668537
X-RAY DIFFRACTIONf_plane_restr0.0084618
X-RAY DIFFRACTIONf_dihedral_angle_d14.92121239
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.582550797249 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.250.32551460.27952316X-RAY DIFFRACTION99.43
2.25-2.350.29651460.25952332X-RAY DIFFRACTION99.32
2.35-2.470.32271440.24762369X-RAY DIFFRACTION99.84
2.47-2.630.30881400.26952329X-RAY DIFFRACTION99.68
2.63-2.830.28861160.25172371X-RAY DIFFRACTION99.76
2.83-3.110.2561950.24372417X-RAY DIFFRACTION99.76
3.12-3.570.24471350.22582368X-RAY DIFFRACTION99.76
3.57-4.490.24151500.18822387X-RAY DIFFRACTION99.72
4.49-43.230.2271250.21362478X-RAY DIFFRACTION99.5
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)
11.423741668920.27358888885-1.983536864752.02392210466-1.874824978363.89544054514-0.0260414309199-0.378266222307-0.01141553602290.5832786778080.05076448577660.02403621912930.06833817331630.4934672030220.10905254370.400797583518-0.0109562122218-0.05444567848440.34102762842-0.01327669941220.268397014727-8.67775427649-11.7912575777-30.69641727
24.32656669935-0.674637443157-0.9363136420872.48663318262-1.090280883843.691586479390.02987068493770.08669865374520.1813681298960.0558613058731-0.07930737735340.183307268955-0.167378237323-0.2065186893210.05705827024640.259294103627-0.0486612163753-0.006809665837420.200315512196-0.04032803203640.210704031908-21.4716718993-8.83330264952-38.2167700744
31.28270853388-0.53033130322-0.9593385349511.59378935885-0.3603801494171.782554665790.05312398276930.2079932683050.0754629617332-0.231220507256-0.1084652346840.0604936310577-0.190788557938-0.1788266592310.07752557027810.16435951060.00840865489079-0.04132810509680.216142651323-0.03864206598020.168715732846-7.12842205839-8.47892581803-59.5461631882
45.335126517980.647607403361-1.314570385714.438088286690.02312283608872.348105623990.103432763919-0.101219094486-0.1108143821960.0908899804068-0.07654846107510.05277819184690.114836477363-0.0550359830385-0.07959459969020.1834819097320.0219988259605-0.001500057674510.1204110798420.0116056845410.0813817139221-2.10689440308-13.3556862018-51.767833829
51.508900261541.31147150135-0.6105361477291.95585926917-1.689222330412.213534878920.1114228325440.04377127002650.2351271498840.2015255186740.01305135442620.223843749151-0.1000353664340.102734069346-0.1838908223480.237277614263-0.01072099712810.009959069139340.147800729041-0.02771094850340.174275402861-8.9890005449-0.459474860174-50.8056273153
65.20660967837-0.04101637131912.545208464331.408626920521.423843267892.80226266015-0.210823294118-1.35716730763-0.3567063498090.5838324796240.05642466761170.267870113390.540800614587-0.3784484067450.2232693009250.6899371182430.04801060296340.06765860922240.5402134209150.008261245682130.281010076113-18.0797745734-5.51492522236-27.3254549481
70.07240825884160.180875280258-0.2141252708993.268629352362.085900762443.07853878811-0.070849617423-0.5484135533660.3749379659520.01645043546680.0989509732505-0.209023632319-0.2996969402660.164004747191-0.06562944850690.341875428409-0.0155424364397-0.06450205745920.434543962134-0.1224628984860.237772671945-2.69766919278-1.41923556692-37.0390365055
82.21806671106-0.4417656310721.096112127221.13088297918-0.3007935419672.33897155990.1332804059530.0455898181457-0.107603168069-0.155543976873-0.08744950292990.069535234783-0.0375249093023-0.181633692079-0.03494039010670.1729924878820.0280881197303-0.03139691630580.180343814867-0.02925746641190.1711905707118.2608352950313.2346506144-11.9987949655
92.988265464341.676467489261.435035243694.259465721163.113797420893.882225751860.135337614534-0.2665529528420.2022474741690.287977371888-0.3867221165410.4608331572540.219469553286-0.1466509653150.229685071650.177905812846-0.0172285276411-0.01796384735960.19419822540.003330363446270.1616659573318.6090903645311.04267409966.54558739604
102.116579541560.5660171172861.377754713081.906101694210.5224653617432.461976454780.07296108865430.2397228679810.020594071802-0.0433664211002-0.02544571601720.0965578777049-0.0331385710160.0947510695108-0.01391687206470.1347650193290.0212013539168-0.02231921466430.215012382751-0.004954705065990.1601108643215.979845088912.0741641488-4.12955582591
112.88100108295-0.420150498371.43836716613.420703757210.7091598046534.033243886510.4548370737090.318206206293-0.180160737593-0.454366703208-0.201055328406-0.01687339013430.445037515794-0.0603163708786-0.2606188753270.2988880482890.04638232803510.004315364685250.292116876455-0.01872765978060.18581209601310.16373834987.47228098623-23.5955085588
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 49 )AA22 - 491 - 28
22chain 'A' and (resid 50 through 98 )AA50 - 9829 - 77
33chain 'A' and (resid 99 through 165 )AA99 - 16578 - 144
44chain 'A' and (resid 166 through 199 )AA166 - 199145 - 178
55chain 'A' and (resid 200 through 218 )AA200 - 218179 - 197
66chain 'A' and (resid 219 through 235 )AA219 - 235198 - 214
77chain 'A' and (resid 236 through 251 )AA236 - 251215 - 230
88chain 'B' and (resid 23 through 139 )BD23 - 1391 - 117
99chain 'B' and (resid 140 through 165 )BD140 - 165118 - 143
1010chain 'B' and (resid 166 through 218 )BD166 - 218144 - 196
1111chain 'B' and (resid 219 through 251 )BD219 - 251197 - 229

+
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