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- PDB-7t50: Crystal structure of the molybdate-binding periplasmic protein Mo... -

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Basic information

Entry
Database: PDB / ID: 7t50
TitleCrystal structure of the molybdate-binding periplasmic protein ModA from the bacteria Pseudomonsa aeruginosa in chromate-bound form
ComponentsMolybdate-binding periplasmic protein ModA
KeywordsMETAL BINDING PROTEIN / Molybdate-binding periplasmic protein
Function / homologyChromate / AMMONIUM ION
Function and homology information
Biological speciesPseudomonas aeruginosa PA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,41311
Polymers48,7592
Non-polymers6549
Water3,927218
1
A: Molybdate-binding periplasmic protein ModA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8087
Polymers24,3791
Non-polymers4286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Molybdate-binding periplasmic protein ModA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6064
Polymers24,3791
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.627, 41.223, 111.366
Angle α, β, γ (deg.)90.000, 92.758, 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 25 through 175 or resid 177 through 321))
d_2ens_1(chain "B" and (resid 25 through 175 or resid 177 through 321))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUVALA1 - 151
d_12ens_1SERLEUA153 - 227
d_13ens_1CQ4CQ4B
d_21ens_1GLUVALH1 - 151
d_22ens_1SERLEUH153 - 227
d_23ens_1CQ4CQ4I

NCS oper: (Code: givenMatrix: (0.999907286567, 0.00362785776747, 0.0131246683078), (0.0033549273622, -0.999778904486, 0.0207578083223), (0.0131970728786, -0.0207118514858, -0.999698382751)Vector: 20. ...NCS oper: (Code: given
Matrix: (0.999907286567, 0.00362785776747, 0.0131246683078), (0.0033549273622, -0.999778904486, 0.0207578083223), (0.0131970728786, -0.0207118514858, -0.999698382751)
Vector: 20.9589717544, 4.69598064105, -55.7723427896)

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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 chromate.
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-CQ4 / Chromate / Dioxido(dioxo)chromium


Mass: 115.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CrO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 2.1 M ammonium sulfate, 20% v/v glycerol

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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: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.9→45.57 Å / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.14 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.065 / Rrim(I) all: 0.122 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1972 / CC1/2: 0.687 / CC star: 0.917 / Rpim(I) all: 0.469 / Rrim(I) all: 0.888 / % possible all: 94.7

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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: 1.9→41.48 Å / SU ML: 0.2295 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5334
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 1636 5 %
Rwork0.2354 31116 -
obs0.2369 32752 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 37 218 3645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923492
X-RAY DIFFRACTIONf_angle_d0.97294737
X-RAY DIFFRACTIONf_chiral_restr0.0568531
X-RAY DIFFRACTIONf_plane_restr0.0063611
X-RAY DIFFRACTIONf_dihedral_angle_d14.85191239
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.717211605034 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.2821332475X-RAY DIFFRACTION95.88
1.95-2.020.34091320.28372573X-RAY DIFFRACTION99.82
2.02-2.090.30971260.27972638X-RAY DIFFRACTION99.82
2.09-2.170.29191710.26142561X-RAY DIFFRACTION99.74
2.17-2.270.31971500.25172601X-RAY DIFFRACTION99.85
2.27-2.390.24861472556X-RAY DIFFRACTION99.41
2.39-2.540.29811530.25092594X-RAY DIFFRACTION99.57
2.54-2.740.30841180.2582597X-RAY DIFFRACTION99.52
2.74-3.010.31841100.2482638X-RAY DIFFRACTION99.21
3.01-3.450.23481340.22372618X-RAY DIFFRACTION99.14
3.45-4.340.20591310.22588X-RAY DIFFRACTION97.74
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)
12.03819832031-0.707008690243-1.077434179172.013819187550.02808336854012.7464564921-0.133410944553-0.392448352437-0.009967282955880.299683910870.06927468198740.08374690624470.05127270366760.0575831027290.05740100013730.192825070482-0.00368115628566-0.005286378814260.251260675445-0.002362387647840.135243794069-16.6795149395-9.64028416519-36.215371139
21.8982510353-0.227073165584-0.4928768620481.605918503740.2199147414982.2050934548-0.01179718512150.151675235675-0.0274659397979-0.263665107673-0.0617319340007-0.0252655063962-0.06571068258810.002401147932030.08076265144710.1590663234580.0145017106042-0.0485640753180.131254223678-0.01084234843530.136357611837-6.88536353275-8.5648383416-59.748410208
31.964653131810.270924374560.05621480363423.820639763880.3714657834423.117591754650.0163552337447-0.0871699408368-0.0769619639490.04537137312140.0107827989442-0.1159264954660.1124608327920.0893931031688-0.03471123752580.103865018896-0.00932173286395-0.01421985525460.118886613510.005288348427850.110815500451-2.60384433776-9.88709393804-53.2626607812
41.62015950483-0.3389609566350.5018803737722.410914356510.9204892598780.897243993479-0.0165064814693-0.8466190446530.09714484959620.3717738332170.13067855306-0.0380302609085-0.05297169738320.174200587353-0.1228559002840.2429386044010.0400437418258-0.02473997497870.374912541557-0.04247780919060.154874221175-11.3293378449-2.95189800838-33.7429336287
51.5551433624-0.2649932318730.4940268743751.87185122839-0.5204607419291.928071092680.1455382138890.384899973511-0.103519366929-0.234906258933-0.2350688426110.0223577229831-0.0745917693160.1215413965430.06188763451210.1988522518070.0821387843621-0.05523234305220.289912748954-0.0357803898580.1791091523687.7885765159616.4195246389-20.9757684346
61.92553509653-0.6300752766350.4747022587471.252643120920.1446904394951.900813367740.1708901785010.234237892169-0.152213422034-0.112913004534-0.1968751441940.2291470518080.167843014998-0.215969314378-0.06821681498340.1524293746160.0245797210657-0.06591392825170.191646750167-0.04258444625650.1865245439386.819026523979.28106358476-10.6062191079
72.888438474970.558244311393-0.1274172328843.057444407510.1180980589621.839482469840.0193088550993-0.2427717007090.05908138807460.280240497113-0.06270678077870.139855833726-0.0748103523916-0.1342622454420.04504932370760.1386438736390.0005670087568-0.03636814706770.194590225729-0.02262285231310.14368089117312.059741378815.34084398133.85803981521
82.18838537993-0.5895603906640.6849274906081.19965851394-1.300070335452.988932092490.15861079480.128776869993-0.233426938212-0.196567331093-0.07003251388630.05053675144280.146538982466-0.0886109733458-0.09324181738430.2122288122090.0508457565664-0.05050701548790.141479991199-0.06367338526430.1651427081912.35345715617.35031719885-10.3469810347
91.898512825250.4022065736512.065488593811.725670357980.6705970818034.052350767220.2909248260620.628984977244-0.283972589661-0.411634953082-0.156782109809-0.09316861695140.4644420624140.471121985152-0.1728759856530.2855430946460.11216599656-0.02573412096340.332842828111-0.07789087240620.22824697066814.19830247836.2964359897-22.4399895063
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 98 )AA25 - 981 - 74
22chain 'A' and (resid 99 through 165 )AA99 - 16575 - 141
33chain 'A' and (resid 166 through 211 )AA166 - 211142 - 187
44chain 'A' and (resid 212 through 251 )AA212 - 251188 - 227
55chain 'B' and (resid 25 through 69 )BH25 - 691 - 45
66chain 'B' and (resid 70 through 120 )BH70 - 12046 - 96
77chain 'B' and (resid 121 through 189 )BH121 - 18997 - 165
88chain 'B' and (resid 190 through 225 )BH190 - 225166 - 201
99chain 'B' and (resid 226 through 251 )BH226 - 251202 - 227

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