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- PDB-3hgm: Universal Stress Protein TeaD from the TRAP transporter TeaABC of... -

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Basic information

Entry
Database: PDB / ID: 3hgm
TitleUniversal Stress Protein TeaD from the TRAP transporter TeaABC of Halomonas elongata
ComponentsUniversal Stress Protein TeaD
KeywordsSIGNALING PROTEIN / universal Stress protein / Rossmann fold
Function / homology
Function and homology information


ATP binding / cytoplasm
Similarity search - Function
Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / TRAP-T-associated universal stress protein TeaD / TRAP-T-associated universal stress protein TeaD
Similarity search - Component
Biological speciesHalomonas elongata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchweikhard, E.S. / Kuhlmann, S.I. / Ziegler, C.M.
CitationJournal: Biochemistry / Year: 2010
Title: Structure and function of the universal stress protein TeaD and its role in regulating the ectoine transporter TeaABC of Halomonas elongata DSM 2581(T)
Authors: Schweikhard, E.S. / Kuhlmann, S.I. / Kunte, H.J. / Grammann, K. / Ziegler, C.M.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
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_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Universal Stress Protein TeaD
B: Universal Stress Protein TeaD
C: Universal Stress Protein TeaD
D: Universal Stress Protein TeaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,11112
Polymers62,9854
Non-polymers2,1268
Water1,72996
1
A: Universal Stress Protein TeaD
B: Universal Stress Protein TeaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5566
Polymers31,4932
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-21 kcal/mol
Surface area15480 Å2
MethodPISA
2
C: Universal Stress Protein TeaD
D: Universal Stress Protein TeaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5566
Polymers31,4932
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-19 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.050, 74.650, 97.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPHEPHEAA1 - 391 - 39
21METMETPHEPHEBB1 - 391 - 39
31METMETPHEPHECC1 - 391 - 39
41METMETPHEPHEDD1 - 391 - 39
12LEULEUGLYGLYAA82 - 9682 - 96
22LEULEUGLYGLYBB82 - 9682 - 96
32LEULEUGLYGLYCC82 - 9682 - 96
42LEULEUGLYGLYDD82 - 9682 - 96
13ARGARGTHRTHRAA109 - 121109 - 121
23ARGARGTHRTHRBB109 - 121109 - 121
33ARGARGTHRTHRCC109 - 121109 - 121
43ARGARGTHRTHRDD109 - 121109 - 121
14GLYGLYVALVALAA130 - 147130 - 147
24GLYGLYVALVALBB130 - 147130 - 147
34GLYGLYVALVALCC130 - 147130 - 147
44GLYGLYVALVALDD130 - 147130 - 147

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Components

#1: Protein
Universal Stress Protein TeaD


Mass: 15746.361 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas elongata (bacteria) / Gene: TeaD / Plasmid: pET 22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D4AEP4, UniProt: E1VBK4*PLUS
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris pH 7.5, 200mM (NH4)2SO4, 15% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 74 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9765 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 43071 / Num. obs: 42968 / % possible obs: 99.8 % / Observed criterion σ(I): 13.21 / Redundancy: 4.8 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.21 / Num. unique all: 3183 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly alanine model of pdb entry 2Z09

2z09


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 9.429 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 2.032 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2166 5 %RANDOM
Rwork0.218 40803 --
obs0.22 40803 99.88 %-
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 max: 63.15 Å2 / Biso mean: 36.271 Å2 / Biso min: 21.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20 Å2
2--0.56 Å20 Å2
3----2.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 128 96 4482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224472
X-RAY DIFFRACTIONr_bond_other_d0.0010.023068
X-RAY DIFFRACTIONr_angle_refined_deg1.0752.0216061
X-RAY DIFFRACTIONr_angle_other_deg0.75937483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5975569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54322.727165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2715783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6121543
X-RAY DIFFRACTIONr_chiral_restr0.0480.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02870
X-RAY DIFFRACTIONr_mcbond_it0.83632829
X-RAY DIFFRACTIONr_mcbond_other0.2931168
X-RAY DIFFRACTIONr_mcangle_it1.46554526
X-RAY DIFFRACTIONr_scbond_it1.65461643
X-RAY DIFFRACTIONr_scangle_it2.78481531
X-RAY DIFFRACTIONr_rigid_bond_restr0.69437540
X-RAY DIFFRACTIONr_sphericity_free2.0873101
X-RAY DIFFRACTIONr_sphericity_bonded0.74737479
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A494TIGHT POSITIONAL0.110.05
B494TIGHT POSITIONAL0.120.05
C494TIGHT POSITIONAL0.10.05
D494TIGHT POSITIONAL0.130.05
A536MEDIUM POSITIONAL0.290.5
B536MEDIUM POSITIONAL0.310.5
C536MEDIUM POSITIONAL0.330.5
D536MEDIUM POSITIONAL0.430.5
A494TIGHT THERMAL0.310.5
B494TIGHT THERMAL0.340.5
C494TIGHT THERMAL0.320.5
D494TIGHT THERMAL0.240.5
A536MEDIUM THERMAL0.212
B536MEDIUM THERMAL0.222
C536MEDIUM THERMAL0.222
D536MEDIUM THERMAL0.192
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 153 -
Rwork0.287 2959 -
all-3112 -
obs--99.58 %
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)
12.6325-1.10960.20541.8219-1.04852.4848-0.0483-0.0843-0.22420.0960.08680.06150.3535-0.0225-0.03850.10010.0067-0.00510.0159-0.00550.038923.45313.904313.825
21.9742-0.4999-1.64131.70250.03972.8810.08140.0740.0884-0.09690.073-0.01980.00430.0168-0.15440.00930.00350.00290.02210.00280.032132.097814.8227-12.0115
31.4675-0.8129-0.15611.66150.32442.7997-0.15650.00310.1930.1073-0.0594-0.0346-0.24070.15160.21580.0916-0.01-0.08790.04750.02380.104849.21-9.971314.1179
41.75520.38110.29483.1543-0.29393.8703-0.05210.0939-0.06640.04480.0283-0.04810.1547-0.11150.02380.0123-0.0041-0.00170.0174-0.01340.021144.9854-10.6074-14.5146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 147
2X-RAY DIFFRACTION2B1 - 147
3X-RAY DIFFRACTION3C1 - 147
4X-RAY DIFFRACTION4D1 - 147

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