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- PDB-3gyy: The ectoine binding protein of the TeaABC TRAP transporter TeaA i... -

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Basic information

Entry
Database: PDB / ID: 3gyy
TitleThe ectoine binding protein of the TeaABC TRAP transporter TeaA in the Apo-State
ComponentsPeriplasmic substrate binding protein
KeywordsTRANSPORT PROTEIN / venus flytrap mechanism
Function / homology
Function and homology information


transmembrane transport / periplasmic space
Similarity search - Function
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
Ectoine-binding periplasmic protein TeaA / Ectoine-binding periplasmic protein TeaA
Similarity search - Component
Biological speciesHalomonas elongata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKuhlmann, S.I. / Terwisscha Van Scheltinga, A.C. / Ziegler, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins
Authors: Marinelli, F. / Kuhlmann, S.I. / Grell, E. / Kunte, H.J. / Ziegler, C. / Faraldo-Gomez, J.D.
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Nov 20, 2013Group: Database references
Revision 1.4Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic substrate binding protein
B: Periplasmic substrate binding protein
C: Periplasmic substrate binding protein
D: Periplasmic substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,52040
Polymers153,1654
Non-polymers2,35536
Water3,855214
1
A: Periplasmic substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7498
Polymers38,2911
Non-polymers4587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,20715
Polymers38,2911
Non-polymers91614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Periplasmic substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7498
Polymers38,2911
Non-polymers4587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Periplasmic substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8159
Polymers38,2911
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.740, 64.980, 121.500
Angle α, β, γ (deg.)90.00, 91.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Periplasmic substrate binding protein / TeaA


Mass: 38291.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas elongata (bacteria) / Gene: teaA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) C41 / References: UniProt: Q8VPB3, UniProt: E1VBK1*PLUS
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris, 50mM zinc acetate, 30% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorDate: Dec 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.2→47.566 Å / Num. all: 57867 / Num. obs: 57867 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.214 / Net I/σ(I): 8.03
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.22 / Num. unique all: 21201 / Num. unique obs: 7165 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vpn

2vpn


Resolution: 2.2→47.566 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.767 / SU ML: 0.37 / σ(I): 2 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2838 2905 5.02 %
Rwork0.2167 --
obs0.2201 57867 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.875 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 233.49 Å2 / Biso mean: 34.53 Å2 / Biso min: 11.94 Å2
Baniso -1Baniso -2Baniso -3
1-4.515 Å2-0 Å20.815 Å2
2---4.194 Å20 Å2
3----0.321 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9820 0 36 214 10070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510059
X-RAY DIFFRACTIONf_angle_d0.81713649
X-RAY DIFFRACTIONf_chiral_restr0.0571453
X-RAY DIFFRACTIONf_plane_restr0.0031823
X-RAY DIFFRACTIONf_dihedral_angle_d16.8513631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1997-2.23580.3271360.27442547X-RAY DIFFRACTION96
2.2358-2.27430.431250.31982609X-RAY DIFFRACTION97
2.2743-2.31570.3321460.2812625X-RAY DIFFRACTION98
2.3157-2.36020.36941390.25412643X-RAY DIFFRACTION99
2.3602-2.40840.32611270.24972658X-RAY DIFFRACTION99
2.4084-2.46070.36031500.23842604X-RAY DIFFRACTION98
2.4607-2.5180.28771370.23242622X-RAY DIFFRACTION98
2.518-2.5810.33741540.22422652X-RAY DIFFRACTION99
2.581-2.65070.34661470.24262593X-RAY DIFFRACTION98
2.6507-2.72870.32541440.24632631X-RAY DIFFRACTION98
2.7287-2.81680.33361380.24252646X-RAY DIFFRACTION98
2.8168-2.91750.30341380.24522598X-RAY DIFFRACTION98
2.9175-3.03420.34151430.23352620X-RAY DIFFRACTION98
3.0342-3.17230.27031490.22862591X-RAY DIFFRACTION98
3.1723-3.33950.27851370.19682629X-RAY DIFFRACTION97
3.3395-3.54870.25561470.19032624X-RAY DIFFRACTION97
3.5487-3.82260.24421280.18062625X-RAY DIFFRACTION97
3.8226-4.2070.24671630.16622549X-RAY DIFFRACTION96
4.207-4.81530.19041150.15822625X-RAY DIFFRACTION96
4.8153-6.06480.22481260.1872621X-RAY DIFFRACTION95
6.0648-47.57730.25321160.22942650X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -29.0054 Å / Origin y: 5.9245 Å / Origin z: -15.7744 Å
111213212223313233
T0.196 Å20.0137 Å2-0.0051 Å2-0.086 Å2-0.0062 Å2--0.1099 Å2
L0.0873 °20.0048 °20.0782 °2--0.0005 °20.0242 °2--0.2782 °2
S0.0097 Å °0.0082 Å °-0.0046 Å °0.0104 Å °0.0308 Å °0.004 Å °0.0322 Å °0.0603 Å °-0.0326 Å °
Refinement TLS groupSelection details: all

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