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- PDB-1sw4: Crystal structure of ProX from Archeoglobus fulgidus in complex w... -

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Basic information

Entry
Database: PDB / ID: 1sw4
TitleCrystal structure of ProX from Archeoglobus fulgidus in complex with trimethyl ammonium
Componentsosmoprotection protein (proX)
KeywordsPROTEIN BINDING / binding-protein / compatible solutes / cation-pi interactions / non-classical hydrogen bonds
Function / homology
Function and homology information


transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / metal ion binding
Similarity search - Function
ProX-like, substrate-binding domain / Osmoprotection protein (prox); domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRAMETHYLAMMONIUM ION / Osmoprotection protein (ProX)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchiefner, A. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis for the binding of compatible solutes by ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus.
Authors: Schiefner, A. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: osmoprotection protein (proX)
B: osmoprotection protein (proX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,93413
Polymers62,2572
Non-polymers67711
Water4,414245
1
A: osmoprotection protein (proX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4346
Polymers31,1281
Non-polymers3065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: osmoprotection protein (proX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5007
Polymers31,1281
Non-polymers3716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.730, 75.740, 66.980
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 6 - 274 / Label seq-ID: 6 - 274

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein osmoprotection protein (proX)


Mass: 31128.305 Da / Num. of mol.: 2 / Mutation: C1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: proX / Plasmid: pASK-IBA6 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(Codon plus RIL) / References: UniProt: O29280
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TMA / TETRAMETHYLAMMONIUM ION


Mass: 74.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: zinc acetate, sodium cacodylate, PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9778 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 49535 / Num. obs: 49535 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28.4 Å2 / Rsym value: 0.086 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.322 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SW1

1sw1


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.08 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24544 2443 4.9 %RANDOM
Rwork0.21619 ---
all0.2176 49535 --
obs0.2176 47096 98.57 %-
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: 23.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.83 Å2
2--1.9 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 17 245 4584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224402
X-RAY DIFFRACTIONr_bond_other_d0.0020.024054
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9815948
X-RAY DIFFRACTIONr_angle_other_deg0.77839472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585538
X-RAY DIFFRACTIONr_chiral_restr0.0760.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024866
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02830
X-RAY DIFFRACTIONr_nbd_refined0.210.2998
X-RAY DIFFRACTIONr_nbd_other0.2370.24933
X-RAY DIFFRACTIONr_nbtor_other0.0830.22804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2283
X-RAY DIFFRACTIONr_metal_ion_refined0.2550.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.216
X-RAY DIFFRACTIONr_mcbond_it0.5871.52692
X-RAY DIFFRACTIONr_mcangle_it1.10524330
X-RAY DIFFRACTIONr_scbond_it1.83431710
X-RAY DIFFRACTIONr_scangle_it3.0724.51618
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
1587medium positional0.10.5
2572loose positional0.435
1587medium thermal0.522
2572loose thermal0.9510
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.412 194
Rwork0.378 3451

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