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- PDB-3m8u: Crystal structure of glutathione-binding protein A (GbpA) from Ha... -

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Basic information

Entry
Database: PDB / ID: 3m8u
TitleCrystal structure of glutathione-binding protein A (GbpA) from Haemophilus parasuis SH0165 in complex with glutathione disulfide (GSSG)
ComponentsHeme-binding protein A
KeywordsTRANSPORT PROTEIN / Glutathione binding protein / ABC-type transport system / periplasmic component
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OXIDIZED GLUTATHIONE DISULFIDE / MALONATE ION / Heme-binding protein A
Similarity search - Component
Biological speciesHaemophilus parasuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsVergauwen, B. / Elegheert, J. / Dansercoer, A. / Devreese, B. / Savvides, S.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Glutathione import in Haemophilus influenzae Rd is primed by the periplasmic heme-binding protein HbpA
Authors: Vergauwen, B. / Elegheert, J. / Dansercoer, A. / Devreese, B. / Savvides, S.N.
History
DepositionMar 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5715
Polymers58,6521
Non-polymers9194
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.520, 68.470, 142.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heme-binding protein A


Mass: 58651.824 Da / Num. of mol.: 1 / Fragment: UNP residues 24-531 / Mutation: P145S, D156M, V210L, F223L, L281H, N351S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parasuis (bacteria) / Strain: serovar 5 (SH0165) / Gene: HAPS_1202, hbpA / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8F653
#2: Chemical ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE


Mass: 612.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32N6O12S2
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M magnesium chloride, 0.1M sodium citrate pH 5.0, 15% w/v PEG 4000 or 4% tacsimate pH4.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9714 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9714 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 48827 / Num. obs: 48793 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.29 % / Biso Wilson estimate: 16.69 Å2 / Rsym value: 0.086 / Net I/σ(I): 19.9
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 7.07 % / Mean I/σ(I) obs: 3.19 / Num. unique all: 3554 / Rsym value: 0.602 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASER2.1.4phasing
PHENIX(phenix.refine: 1.6.1_340)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DPP

1dpp


Resolution: 1.85→38.995 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 15.89 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 2440 5 %RANDOM
Rwork0.1583 ---
all0.1598 48827 --
obs0.1598 48787 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.664 Å2 / ksol: 0.414 e/Å3
Displacement parametersBiso mean: 20.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.043 Å20 Å2-0 Å2
2--0.399 Å2-0 Å2
3----0.442 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 61 594 4681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064282
X-RAY DIFFRACTIONf_angle_d0.9915820
X-RAY DIFFRACTIONf_dihedral_angle_d13.9951634
X-RAY DIFFRACTIONf_chiral_restr0.066617
X-RAY DIFFRACTIONf_plane_restr0.011766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8498-1.88750.24011390.19882654X-RAY DIFFRACTION100
1.8875-1.92850.24111420.19152691X-RAY DIFFRACTION100
1.9285-1.97340.20571420.182699X-RAY DIFFRACTION100
1.9734-2.02280.2111410.1762671X-RAY DIFFRACTION100
2.0228-2.07740.18891430.1652721X-RAY DIFFRACTION100
2.0774-2.13860.22491420.15552688X-RAY DIFFRACTION100
2.1386-2.20760.20011410.1582687X-RAY DIFFRACTION100
2.2076-2.28650.17141430.15442712X-RAY DIFFRACTION100
2.2865-2.3780.17351420.15572698X-RAY DIFFRACTION100
2.378-2.48620.20441430.15472714X-RAY DIFFRACTION100
2.4862-2.61730.17231420.15412714X-RAY DIFFRACTION100
2.6173-2.78120.2211440.15242722X-RAY DIFFRACTION100
2.7812-2.99590.17231440.15032743X-RAY DIFFRACTION100
2.9959-3.29720.17791440.15142740X-RAY DIFFRACTION100
3.2972-3.7740.17971450.14042758X-RAY DIFFRACTION100
3.774-4.75350.15141480.12532807X-RAY DIFFRACTION100
4.7535-39.00340.1881550.18722928X-RAY DIFFRACTION100
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)
11.4196-0.45530.07670.72530.5040.54680.0557-0.08410.15290.0066-0.0306-0.01030.0539-0.0315-0.02230.11450.00660.03260.0908-0.01120.096316.70765.956-21.5859
20.36230.1933-0.2050.3677-0.13940.1749-0.02680.06020.0115-0.12520.0277-0.0090.06-0.03760.00280.0936-0.0003-0.00170.0605-0.00360.04917.5468-16.7531-32.4218
30.07090.0751-0.12340.437-0.08720.2291-0.0730.024-0.0293-0.16920.013-0.03310.1287-0.07350.0330.1611-0.02560.00320.0775-0.02320.06914.898-26.9476-34.07
40.27830.1323-0.12080.36260.06890.11210.0427-0.02770.0393-0.0331-0.0158-0.0116-0.02110.0515-0.02390.0695-0.00960.01070.06610.00070.059122.4209-5.1304-22.0433
50.1246-0.0086-0.19490.3911-0.12380.44360.0696-0.05250.0156-0.0422-0.04640.0529-0.03270.0485-0.02070.0593-0.00660.0080.0606-0.01640.072511.0005-17.959-5.6636
60.3275-0.02860.05070.7848-0.60790.4714-0.0074-0.131-0.0285-0.09790.0585-0.02140.0652-0.0387-0.02620.05580.00270.02250.05680.00690.04769.5412-30.58072.3875
70.4628-0.26120.76850.2257-0.58922.343-0.0327-0.1286-0.09770.01940.0140.0304-0.0626-0.18440.00330.0985-0.0081-0.00280.12140.02380.11021.3073-31.9052-3.3173
80.2366-0.1430.0570.32480.1030.09120.0001-0.08480.0190.0354-0.0132-0.07610.05880.11320.02080.06270.0246-0.0010.0980.02430.0620.9683-31.11071.6571
90.32620.0685-0.17780.016-0.07620.489-0.02410.0086-0.0395-0.0163-0.00350.04270.1025-0.04110.0170.0632-0.0118-0.00890.0497-0.01740.06618.1379-27.1573-15.453
100.46150.40510.22880.36210.20460.11720.04790.0625-0.28570.1051-0.00450.0910.04660.0027-0.04250.21090.04510.02990.0708-0.03470.28419.00487.8226-20.3726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 24:27)A24 - 27
2X-RAY DIFFRACTION2(chain A and resid 28:132)A28 - 132
3X-RAY DIFFRACTION3(chain A and resid 133:182)A133 - 182
4X-RAY DIFFRACTION4(chain A and resid 183:270)A183 - 270
5X-RAY DIFFRACTION5(chain A and resid 271:299)A271 - 299
6X-RAY DIFFRACTION6(chain A and resid 300:331)A300 - 331
7X-RAY DIFFRACTION7(chain A and resid 332:355)A332 - 355
8X-RAY DIFFRACTION8(chain A and resid 356:421)A356 - 421
9X-RAY DIFFRACTION9(chain A and resid 422:527)A422 - 527
10X-RAY DIFFRACTION10(chain A and resid 528:531)A528 - 531

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