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- PDB-2vpn: High-resolution structure of the periplasmic ectoine-binding prot... -

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Basic information

Entry
Database: PDB / ID: 2vpn
TitleHigh-resolution structure of the periplasmic ectoine-binding protein from TeaABC TRAP-transporter of Halomonas elongata
ComponentsPERIPLASMIC SUBSTRATE BINDING PROTEIN
KeywordsTRANSPORT / ECTOINE / HYDROXYECTOINE / TRAP-TRANSPORTER / PERIPLASMIC BINDING PROTEIN
Function / homology
Function and homology information


organic substance transport / 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
Chem-4CS / Ectoine-binding periplasmic protein TeaA / Ectoine-binding periplasmic protein TeaA
Similarity search - Component
Biological speciesHALOMONAS ELONGATA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsKuhlmann, S.I. / Terwisscha van Scheltinga, A.C. / Bienert, R. / Kunte, H.J. / Ziegler, C.
CitationJournal: Biochemistry / Year: 2008
Title: 1.55 A Structure of the Ectoine Binding Protein Teaa of the Osmoregulated Trap-Transporter Teaabc from Halomonas Elongata.
Authors: Kuhlmann, S.I. / Terwisscha Van Scheltinga, A.C. / Bienert, R. / Kunte, H.J. / Ziegler, C.
History
DepositionMar 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_conn.ptnr2_symmetry
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,90512
Polymers71,4262
Non-polymers47910
Water11,980665
1
A: PERIPLASMIC SUBSTRATE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9536
Polymers35,7131
Non-polymers2395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PERIPLASMIC SUBSTRATE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9536
Polymers35,7131
Non-polymers2395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.300, 52.200, 63.500
Angle α, β, γ (deg.)80.80, 85.80, 77.90
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 41
2112B1 - 41
1212A47 - 154
2212B47 - 154
1312A165 - 311
2312B165 - 311
1415A42 - 46
2415B42 - 46
1514A154 - 165
2514B154 - 165

NCS oper: (Code: given
Matrix: (-0.8924, 0.3868, 0.2323), (-0.3719, -0.9221, 0.1067), (0.2555, 0.0088, 0.9668)
Vector: 62.04, 88.7783, -39.9572)

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Components

#1: Protein PERIPLASMIC SUBSTRATE BINDING PROTEIN / ECTOINE-PERIPLASMIC BINDING PROTEIN


Mass: 35713.223 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HALOMONAS ELONGATA (bacteria) / Strain: DSM 2581T / Plasmid: PET 26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VPB3, UniProt: E1VBK1*PLUS
#2: Chemical ChemComp-4CS / (4S)-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / ECTOINE / Ectoine


Mass: 142.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N2O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details(4S)-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID (4CS): ECTOINE

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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: 2.14 Å3/Da / Density % sol: 42.68 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 0.1 M MGCL2 AND 25.5 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9781
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 6, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. obs: 81024 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 9.2
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 2.3 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.46 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1606 2 %RANDOM
Rwork0.158 ---
obs0.159 79385 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.41 Å2-0.56 Å2
2---0.41 Å20.02 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4911 0 28 665 5604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225299
X-RAY DIFFRACTIONr_bond_other_d0.0020.023487
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9567228
X-RAY DIFFRACTIONr_angle_other_deg0.95738600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25226.421285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30615899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4781510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026112
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021026
X-RAY DIFFRACTIONr_nbd_refined0.2280.21073
X-RAY DIFFRACTIONr_nbd_other0.1820.23668
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22677
X-RAY DIFFRACTIONr_nbtor_other0.0840.22700
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2491
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.13134206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.61955217
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.22462430
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.20281998
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1612tight positional0.070.05
2138medium positional0.370.5
7loose positional0.565
1612tight thermal0.180.5
2138medium thermal0.772
7loose thermal4.6410
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 133
Rwork0.201 5718

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