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- PDB-4pcd: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4pcd
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS OCh 114 (RD1_1052, TARGET EFI-510238) WITH BOUND L-GALACTONATE
ComponentsC4-dicarboxylate transport system, substrate-binding protein, putative
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-galactonic acid / Solute-binding protein RD1_1052
Similarity search - Component
Biological speciesRoseobacter denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Aug 26, 2015Group: Data collection
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C4-dicarboxylate transport system, substrate-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2632
Polymers36,0671
Non-polymers1961
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.375, 73.260, 75.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein C4-dicarboxylate transport system, substrate-binding protein, putative


Mass: 36066.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseobacter denitrificans (bacteria) / Strain: OCh 114 / Gene: RD1_1052 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16BC9
#2: Chemical ChemComp-2Q2 / L-galactonic acid


Mass: 196.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (42.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-MANNONATE); Reservoir (0.1 M Tris pH 8.5, 2.4 M di-Ammonium Phosphate); Cryoprotection (80% Reservoir + 20% diethylene glycol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 2, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→75.89 Å / Num. obs: 32764 / % possible obs: 99.8 % / Redundancy: 11.7 % / Biso Wilson estimate: 13.86 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.041 / Net I/σ(I): 16 / Num. measured all: 383228 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.7-1.7311.90.7265.12035917100.21899.9
9-75.896.30.08520.212882060.03473.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→42.607 Å / FOM work R set: 0.9211 / SU ML: 0.11 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 14.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1791 3129 5.06 %
Rwork0.1354 58718 -
obs0.1376 61847 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.26 Å2 / Biso mean: 18.38 Å2 / Biso min: 5.55 Å2
Refinement stepCycle: final / Resolution: 1.7→42.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 13 346 2669
Biso mean--13.31 31.86 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122393
X-RAY DIFFRACTIONf_angle_d1.1863254
X-RAY DIFFRACTIONf_chiral_restr0.07371
X-RAY DIFFRACTIONf_plane_restr0.006429
X-RAY DIFFRACTIONf_dihedral_angle_d13.85893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72660.19231240.168226732797100
1.7266-1.75490.19421400.156826642804100
1.7549-1.78510.1921320.1626992831100
1.7851-1.81760.20841300.151826942824100
1.8176-1.85260.21721640.142826462810100
1.8526-1.89040.15911320.140626832815100
1.8904-1.93150.17531610.135626932854100
1.9315-1.97640.19311540.122826092763100
1.9764-2.02580.14521220.120827342856100
2.0258-2.08060.13481530.121426492802100
2.0806-2.14180.19081240.120327162840100
2.1418-2.2110.14571630.113326452808100
2.211-2.290.19121350.118527142849100
2.29-2.38160.14941350.115926782813100
2.3816-2.490.16691670.123226332800100
2.49-2.62130.14341550.117526932848100
2.6213-2.78550.17151470.132226662813100
2.7855-3.00050.17361160.136527042820100
3.0005-3.30240.22131320.147227052837100
3.3024-3.780.18611570.139526522809100
3.78-4.76140.15911360.125626772813100
4.7614-42.61990.22521500.17132491264194
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)
11.35170.11540.74191.03230.49032.1233-0.00190.15940.1773-0.1473-0.04720.0732-0.1611-0.00010.00580.0998-0.00790.00550.10360.03530.08851.142832.75417.5432
20.65550.06790.07920.3574-0.22090.8154-0.01020.02260.2149-0.014-0.01450.0018-0.2266-0.06560.02170.11260.0037-0.01150.06790.01730.106545.119738.181224.2997
30.99010.05120.28690.86490.07421.18520.019-0.0913-0.06170.072-0.0494-0.07320.11920.02850.04640.1039-0.00340.00210.1122-0.00260.110747.645823.817640.3223
40.9470.07810.3530.47160.05520.94610.0083-0.09540.16660.0345-0.01690.0018-0.0893-0.0090.01660.08290.00030.00370.0674-0.01950.09352.947434.670240.517
52.11760.13211.04790.83280.30881.65930.10990.1713-0.0934-0.01450.0065-0.07060.13520.2103-0.07540.08340.0040.01980.07010.01310.072257.023225.228625.7473
62.48370.6268-0.66921.1937-0.36911.21-0.0312-0.2137-0.16040.126-0.0449-0.13540.00360.12990.06470.1459-0.0182-0.02490.1263-0.01610.110760.047129.540451.6196
75.1797-0.48430.56083.28250.24753.1602-0.0972-0.3091-0.06950.1694-0.05670.1747-0.0683-0.41920.07510.1491-0.04270.00390.17380.02040.140842.399820.842650.0546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 58 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 93 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 124 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 251 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 252 through 286 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 287 through 310 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 311 through 324 )A0

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