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- PDB-7t51: Crystal structure of the molybdate-binding periplasmic protein Mo... -

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Basic information

Entry
Database: PDB / ID: 7t51
TitleCrystal structure of the molybdate-binding periplasmic protein ModA from the bacteria Pseudomonsa aeruginosa in molybdate-bound form
ComponentsMolybdate-binding periplasmic protein ModA
KeywordsMETAL BINDING PROTEIN / Molybdate-binding periplasmic protein
Function / homologyMOLYBDATE ION / AMMONIUM ION
Function and homology information
Biological speciesPseudomonas aeruginosa PA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)49,1896
Polymers48,7592
Non-polymers4304
Water93752
1
A: Molybdate-binding periplasmic protein ModA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5573
Polymers24,3791
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Molybdate-binding periplasmic protein ModA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6313
Polymers24,3791
Non-polymers2522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.528, 40.898, 111.090
Angle α, β, γ (deg.)90.000, 92.543, 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 251 or resid 323))
d_2ens_1(chain "B" and (resid 25 through 251 or resid 323))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLULEUA1 - 227
d_12ens_1MOOMOOC
d_21ens_1GLULEUD1 - 227
d_22ens_1MOOMOOF

NCS oper: (Code: givenMatrix: (0.999964244802, -0.000100921658709, 0.00845570417551), (-0.000226516651797, -0.999889652868, 0.0148536452729), (0.00845327205828, -0.0148550295357, -0.999853924475) ...NCS oper: (Code: given
Matrix: (0.999964244802, -0.000100921658709, 0.00845570417551), (-0.000226516651797, -0.999889652868, 0.0148536452729), (0.00845327205828, -0.0148550295357, -0.999853924475)
Vector: 20.7338107975, 4.4151969857, -55.6164514874)

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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 molybdate.
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-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: MoO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.99 Å3/Da / Density % sol: 38.2 %
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, 25% v/v glycerol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX110.954
SYNCHROTRONAustralian Synchrotron MX120.954
Detector
TypeIDDetectorDate
DECTRIS EIGER2 X 9M1PIXELSep 21, 2019
DECTRIS EIGER2 X 9M2PIXELSep 21, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9541
21
ReflectionResolution: 2.5→45.48 Å / Num. obs: 13730 / % possible obs: 94.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 22.7 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.054 / Rrim(I) all: 0.099 / Χ2: 1.02 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1155 / CC1/2: 0.906 / CC star: 0.969 / Rpim(I) all: 0.177 / Rrim(I) all: 0.307 / Χ2: 1.08 / % possible all: 71.5

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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: 2.5→45.48 Å / SU ML: 0.3239 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2886 663 4.84 %
Rwork0.2587 13022 -
obs0.2601 13685 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 17 52 3459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833473
X-RAY DIFFRACTIONf_angle_d1.23164715
X-RAY DIFFRACTIONf_chiral_restr0.0589530
X-RAY DIFFRACTIONf_plane_restr0.0055610
X-RAY DIFFRACTIONf_dihedral_angle_d14.33641230
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.729205354878 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.37911030.30592050X-RAY DIFFRACTION74.76
2.69-2.960.33771340.30062701X-RAY DIFFRACTION99.75
2.96-3.390.291180.27542767X-RAY DIFFRACTION99.65
3.39-4.270.26731510.23642711X-RAY DIFFRACTION99.24
4.28-45.480.26431570.23332793X-RAY DIFFRACTION98.53
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)
14.85228635709-0.815072120853-0.7799428050523.450701365731.622462990912.94016579029-0.152097164941-0.6234508089850.01388314396650.4459398435040.0791138296408-0.258471034525-0.0515984961290.3438513401050.0372107122980.314790004061-0.0664985488115-0.0669787601360.159597012540.05161573499670.234478458286-7.96720521862-11.3136688941-31.9757588834
20.710647058623-0.254242844219-0.1599341464441.323182486740.2977404643110.2142757063520.0645557273592-0.376294780966-0.03559619381220.2869312370340.018278506515-0.04625315393350.06036757712740.234858901011-0.0656724318870.225828967568-0.0414147420577-0.02834035559750.167318042985-0.005439263078990.0752908165239-18.9499798505-12.1104178144-37.7442210731
32.50846256820.7562428522031.677141007250.7397853714980.8843156902265.2895900009-0.467723352629-0.5241302951980.282932250901-0.3107647534850.0887590418230.298685367022-0.6763083885530.6016257528450.02787891725840.3200289080860.01351265747280.09311518441430.265352221056-0.0009451155793010.237412987318-25.8146536017-2.05307037882-39.0621561042
41.62570622572-0.1112488904360.04474602916091.190764919880.5009955327370.470656170909-0.08607554536750.3275260796950.119629709956-0.159079437963-0.0535408286012-0.0598524677058-0.288637102678-0.0824778397182-0.2299037720670.150131510497-0.00622675373087-0.02355714963150.101061555039-0.03748159195040.0449042366589-4.30673168413-9.09947402716-58.1203491673
50.4466310899620.186292794087-0.3332428476030.564288197629-0.2948428405630.634454062159-0.1066162259420.106685779083-0.126297505777-0.176040080037-0.0715435678270.00370596834750.0769105209852-0.0714876894212-0.7890623830180.1145919380160.00152131131636-0.0329347225189-0.0436569484179-0.05547700585460.0468397781062-11.9418828058-7.56350729031-62.117579213
60.3098643334710.3589862901540.3469131985752.54150214957-0.4814763351430.7641209464190.04766603062770.147640597840.0735378220845-0.0972526263740.0744870873769-0.2108054999690.1352155843110.04284703451950.440722278530.2219366336720.03948282203130.09699251814660.1100162958770.06602925801990.133903755976-2.10498223113-10.6250953831-53.1122066175
70.9542290570730.311053443694-0.145717019531.60824472004-0.276674345613.653529690090.206763217675-0.2063119666070.09686347681530.28729321081-0.2722203089180.30253307435-0.263829682983-0.5750999811610.1393586861360.321031026409-0.07935404368550.008412321722270.278269851593-0.1650116395020.251256114471-18.4577654364-3.08682865712-37.9447196839
81.3095325256-0.665935055056-0.6280282714741.190700286990.8082248484480.585478152576-0.0970787339375-0.5352221115040.2170179013380.3795938896620.160311304533-0.174291773866-0.2883405363760.257561429073-0.1480176849220.3896128186310.0209101556721-0.04314645645190.365285648394-0.1083829179410.197529697199-6.35974221984-2.32815196059-33.3195291363
92.39767318657-0.04315976122380.3435052121321.35484636983-0.145065962131.24141638813-0.03222778973020.0947816760355-0.133329233782-0.154142641977-0.04113636551230.12137972514-0.110799194826-0.07055868242930.05484134556670.2389942602910.0374048879279-0.03944042168740.128030569681-0.021897207490.1378601785158.0658690164113.130691971-11.671316171
101.914353607480.239671467047-0.07658633997510.7024022701130.0431640025071.459315061620.08842257519050.101878729755-0.0569292665543-0.22110108126-0.0852672152210.03106611254720.0399408124581-0.01416691772470.01853951185040.310430790140.0274022520857-0.05784167102660.0851127144122-0.02110753201150.094956974455612.401438347410.5877668827-7.48551997049
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 49 )AA25 - 491 - 25
22chain 'A' and (resid 50 through 81 )AA50 - 8126 - 57
33chain 'A' and (resid 82 through 98 )AA82 - 9858 - 74
44chain 'A' and (resid 99 through 139 )AA99 - 13975 - 115
55chain 'A' and (resid 140 through 165 )AA140 - 165116 - 141
66chain 'A' and (resid 166 through 208 )AA166 - 208142 - 184
77chain 'A' and (resid 209 through 225 )AA209 - 225185 - 201
88chain 'A' and (resid 226 through 251 )AA226 - 251202 - 227
99chain 'B' and (resid 25 through 139 )BD25 - 1391 - 115
1010chain 'B' and (resid 140 through 251 )BD140 - 251116 - 227

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